Variant report

Variant	rs6461986
Chromosome Location	chr7:27158496-27158497
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:27154475-27158869	PANC-1	pancreas:	n/a	n/a
2	CHD1	chr7:27152421-27165798	IMR90	lung:	n/a	n/a
3	POLR2A	chr7:27154591-27158719	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr7:27152538-27159551	IMR90	lung:	n/a	n/a
5	POLR2A	chr7:27156770-27158567	A549	lung:	n/a	n/a
6	POLR2A	chr7:27158097-27158514	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:27156578-27158562	HUVEC	blood vessel:	n/a	n/a
8	CEBPB	chr7:27157796-27158592	IMR90	lung:	n/a	chr7:27158082-27158094
9	POLR2A	chr7:27157159-27158600	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr7:27157752-27158680	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
HOXA-AS2	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10256787	0.81[AFR][1000 genomes]
rs17437258	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17500654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17500925	0.81[AFR][1000 genomes]
rs1859162	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1978133	0.89[EUR][1000 genomes]
rs1989935	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2158218	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4722658	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4722660	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4722662	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6461988	0.83[EUR][1000 genomes]
rs6943542	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6944345	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6944900	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6958882	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6962892	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs929247	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs929248	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
6	nsv824038	chr7:27119294-27284522	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
7	nsv887857	chr7:27120689-27229549	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv824039	chr7:27121825-27294951	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
9	nsv824040	chr7:27121870-27295010	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
10	nsv887858	chr7:27127231-27188659	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
11	nsv887860	chr7:27127231-27196069	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
12	nsv887859	chr7:27127231-27196113	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
13	nsv887861	chr7:27127231-27206688	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
14	nsv887862	chr7:27127231-27217359	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
15	nsv887863	chr7:27127231-27243106	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
16	nsv887864	chr7:27127231-27243962	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
17	nsv887865	chr7:27127231-27247279	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
18	nsv887866	chr7:27127231-27248373	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
19	nsv887867	chr7:27127231-27252246	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
20	nsv824041	chr7:27128039-27294951	Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases
21	nsv606463	chr7:27135314-27182245	Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
22	nsv887868	chr7:27135314-27202289	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
23	nsv887869	chr7:27135314-27297791	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
24	nsv887871	chr7:27136308-27179814	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
25	nsv887872	chr7:27136308-27181437	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
26	nsv887873	chr7:27136308-27186495	Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
27	nsv887874	chr7:27136308-27196069	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
28	nsv606464	chr7:27138478-27168590	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
29	nsv1020608	chr7:27139892-27324004	Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
30	nsv538807	chr7:27139892-27324004	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
31	nsv1033316	chr7:27140645-27237951	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
32	nsv606465	chr7:27143757-27229549	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	174 gene(s)	inside rSNPs	diseases
33	nsv606466	chr7:27145024-27197319	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
34	nsv606467	chr7:27145100-27196113	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
35	nsv887875	chr7:27145100-27243962	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
36	nsv532118	chr7:27146920-27354205	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
37	nsv5674	chr7:27152562-27197341	Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27145800-27162800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr7:27146400-27169600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:27146800-27159000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:27151600-27159200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr7:27152800-27169400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:27154600-27158600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
7	chr7:27155200-27159400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr7:27155200-27163600	Weak transcription	NHDF-Ad	bronchial
9	chr7:27155400-27159800	Genic enhancers	Fetal Muscle Leg	muscle
10	chr7:27155400-27161600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:27155600-27169400	Weak transcription	Hela-S3	cervix
12	chr7:27156200-27161600	Weak transcription	Gastric	stomach
13	chr7:27156200-27169200	Weak transcription	Osteobl	bone
14	chr7:27156400-27158600	Flanking Active TSS	Colonic Mucosa	Colon
15	chr7:27156400-27158600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
16	chr7:27156600-27158600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr7:27156600-27161600	Weak transcription	NHEK	skin
18	chr7:27156800-27158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:27157000-27158600	Bivalent/Poised TSS	Fetal Brain Male	brain
20	chr7:27157000-27158600	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr7:27157000-27159600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:27157200-27158600	Active TSS	Lung	lung
23	chr7:27157200-27159200	Flanking Active TSS	HUVEC	blood vessel
24	chr7:27157400-27158600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr7:27157400-27160600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr7:27157600-27158600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
27	chr7:27157600-27158600	Transcr. at gene 5' and 3'	A549	lung
28	chr7:27157800-27158600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr7:27157800-27158600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
30	chr7:27157800-27159400	Enhancers	Spleen	Spleen
31	chr7:27158000-27158600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:27158000-27158600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:27158000-27158600	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
34	chr7:27158000-27158600	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr7:27158000-27159000	Weak transcription	Psoas Muscle	Psoas
36	chr7:27158000-27160400	Weak transcription	Right Atrium	heart
37	chr7:27158000-27161000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr7:27158200-27158600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:27158200-27158600	Enhancers	HMEC	breast
40	chr7:27158200-27159200	Weak transcription	Stomach Mucosa	stomach
41	chr7:27158200-27159400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:27158200-27159400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:27158200-27159800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr7:27158200-27161000	Enhancers	Small Intestine	intestine
45	chr7:27158400-27158600	Flanking Bivalent TSS/Enh	NH-A	brain
46	chr7:27158400-27158800	Flanking Active TSS	Fetal Stomach	stomach
47	chr7:27158400-27159000	Enhancers	HepG2	liver
48	chr7:27158400-27159200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:27158400-27160200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:27158400-27160400	Enhancers	NHLF	lung

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