Variant report

Variant	rs2522827
Chromosome Location	chr7:27143540-27143541
allele	C/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	SUZ12	chr7:27140467-27147000	NT2-D1	testis:	n/a	n/a
2	POLR2A	chr7:27140166-27143643	HUVEC	blood vessel:	n/a	n/a
3	RAD21	chr7:27143157-27143760	IMR90	lung:	n/a	chr7:27143404-27143418
4	STAT3	chr7:27143313-27143553	MCF10A-Er-Src	breast:	n/a	chr7:27143480-27143491 chr7:27143479-27143493 chr7:27143486-27143493 chr7:27143476-27143496 chr7:27143482-27143491 chr7:27143481-27143490
5	CTBP2	chr7:27143049-27143800	H1-hESC	embryonic stem cell:	n/a	n/a
6	SUZ12	chr7:27140392-27143704	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr7:27143403-27143541	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr7:27143139-27143685	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr7:27135386-27149832	IMR90	lung:	n/a	n/a
10	POLR2A	chr7:27143036-27144103	PANC-1	pancreas:	n/a	n/a
11	TCF7L2	chr7:27143306-27143664	PANC-1	pancreas:	n/a	n/a
12	ELF1	chr7:27143488-27143733	K562	blood:	n/a	chr7:27143684-27143695 chr7:27143684-27143695 chr7:27143685-27143694
13	POLR2A	chr7:27139372-27143752	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr7:27143339-27143712	MCF10A-Er-Src	breast:	n/a	chr7:27143480-27143491 chr7:27143479-27143493 chr7:27143486-27143493 chr7:27143476-27143496 chr7:27143482-27143491 chr7:27143542-27143554 chr7:27143481-27143490
15	STAT3	chr7:27143319-27143674	MCF10A-Er-Src	breast:	n/a	chr7:27143480-27143491 chr7:27143479-27143493 chr7:27143486-27143493 chr7:27143476-27143496 chr7:27143482-27143491 chr7:27143542-27143554 chr7:27143481-27143490
16	CHD1	chr7:27134717-27152399	IMR90	lung:	n/a	chr7:27141647-27141657
17	MYC	chr7:27143370-27143560	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr7:27143097-27143887	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27142592..27146221-chr7:27150482..27153856,3	K562	blood:
2	chr7:27142771..27145430-chr7:27145468..27147720,2	K562	blood:
3	7:27143270-27156413..7:27162022-27164727	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
HOXA-AS2	TF binding region
HOXA2	TF binding region
ENSG00000253552	Chromatin interaction
ENSG00000105997	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2522828	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706017	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706018	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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	nsv887870	chr7:27136308-27154737	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2522827	HOTAIRM1	cis	Whole Blood	GTEx
rs2522827	HOTAIRM1	cis	Thyroid	GTEx
rs2522827	HOTAIRM1	cis	lung	GTEx
rs2522827	HOXA2	Cis_1M	lymphoblastoid	RTeQTL
rs2522827	HOTAIRM1	cis	Skin Sun Exposed Lower leg	GTEx
rs2522827	HOTAIRM1	cis	Esophagus Muscularis	GTEx
rs2522827	HOTAIRM1	cis	Artery Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27137000-27146800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:27137600-27149000	Weak transcription	HepG2	liver
3	chr7:27138000-27144200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:27138000-27144800	Weak transcription	A549	lung
5	chr7:27140200-27143800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr7:27140200-27144200	Active TSS	Aorta	Aorta
7	chr7:27140200-27144800	Flanking Active TSS	HUVEC	blood vessel
8	chr7:27140400-27143600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:27140400-27143800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
10	chr7:27140400-27143800	Active TSS	Esophagus	oesophagus
11	chr7:27140400-27144200	Active TSS	Colon Smooth Muscle	Colon
12	chr7:27140600-27143600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
13	chr7:27140600-27143800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:27140600-27144200	Active TSS	Rectal Smooth Muscle	rectum
15	chr7:27140800-27143600	Active TSS	Colonic Mucosa	Colon
16	chr7:27140800-27143800	Active TSS	Psoas Muscle	Psoas
17	chr7:27140800-27144200	Active TSS	Right Atrium	heart
18	chr7:27141000-27143600	Active TSS	Fetal Stomach	stomach
19	chr7:27141000-27143800	Active TSS	Placenta Amnion	Placenta Amnion
20	chr7:27141000-27145600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr7:27141400-27143800	Active TSS	Stomach Mucosa	stomach
22	chr7:27141400-27144200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:27141400-27144400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr7:27141400-27145400	Weak transcription	HSMMtube	muscle
25	chr7:27141400-27146000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:27141400-27146000	Weak transcription	HSMM	muscle
27	chr7:27141600-27144000	Weak transcription	Osteobl	bone
28	chr7:27141600-27144200	Enhancers	Spleen	Spleen
29	chr7:27141600-27144400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr7:27141600-27144400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr7:27142000-27143800	Flanking Active TSS	NHEK	skin
32	chr7:27142200-27144000	Flanking Active TSS	HMEC	breast
33	chr7:27142400-27143600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
34	chr7:27142400-27143800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr7:27142400-27144600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:27142400-27144600	Flanking Active TSS	NHLF	lung
37	chr7:27142400-27146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:27142600-27143800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:27142600-27143800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:27142600-27143800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
41	chr7:27142600-27143800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr7:27142600-27147600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:27142800-27143600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:27142800-27149000	Weak transcription	NHDF-Ad	bronchial
45	chr7:27143000-27143600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:27143000-27143600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:27143000-27143600	Active TSS	Fetal Kidney	kidney
48	chr7:27143000-27143600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr7:27143000-27143600	Enhancers	Lung	lung
50	chr7:27143200-27143600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links