Variant report

Variant	rs6836952
Chromosome Location	chr4:1166009-1166010
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	GABPA	chr4:1165491-1166425	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:1165943-1166592	PFSK-1	brain:	n/a	n/a
3	CTBP2	chr4:1165160-1166154	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:1159180-1166648	PFSK-1	brain:	n/a	n/a
5	E2F6	chr4:1165984-1166656	H1-hESC	embryonic stem cell:	n/a	chr4:1166189-1166199
6	GABPA	chr4:1166009-1166465	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1160471..1164177-chr4:1164804..1166602,3	K562	blood:

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000273179	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10008164	1.00[EUR][1000 genomes]
rs10013662	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11932230	1.00[EUR][1000 genomes]
rs1250087	1.00[EUR][1000 genomes]
rs1250127	1.00[EUR][1000 genomes]
rs1272043	1.00[EUR][1000 genomes]
rs1383658	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1481168	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1680077	1.00[EUR][1000 genomes]
rs1871758	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2127909	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2127911	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28392476	1.00[EUR][1000 genomes]
rs36084010	1.00[EUR][1000 genomes]
rs4246689	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4336168	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4465987	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4974567	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4974626	1.00[EUR][1000 genomes]
rs4974634	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4974635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4974636	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4974641	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4974645	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57106389	1.00[EUR][1000 genomes]
rs58168130	1.00[EUR][1000 genomes]
rs58780485	1.00[EUR][1000 genomes]
rs59758572	1.00[EUR][1000 genomes]
rs61053739	1.00[EUR][1000 genomes]
rs6834402	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6836809	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7659524	1.00[EUR][1000 genomes]
rs7660109	0.89[AMR][1000 genomes]
rs7676912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7691582	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs900031	1.00[EUR][1000 genomes]
rs922697	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
12	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
14	nsv519106	chr4:1158991-1174861	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
16	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
19	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
20	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1162000-1166200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:1164000-1167000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
3	chr4:1164200-1166400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:1164200-1167200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
5	chr4:1164400-1166200	Bivalent Enhancer	Fetal Brain Male	brain
6	chr4:1164400-1167200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:1164600-1166200	Flanking Active TSS	Right Ventricle	heart
8	chr4:1164600-1166400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:1164600-1166400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
10	chr4:1164600-1166600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
11	chr4:1164600-1166600	Bivalent/Poised TSS	Fetal Brain Female	brain
12	chr4:1164600-1166600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
13	chr4:1164600-1166800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:1164800-1166600	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
15	chr4:1164800-1166600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:1164800-1166800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:1164800-1166800	Active TSS	NHDF-Ad	bronchial
18	chr4:1164800-1167000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr4:1165000-1166200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
20	chr4:1165000-1166400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr4:1165000-1166400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
22	chr4:1165000-1166400	Active TSS	Right Atrium	heart
23	chr4:1165000-1166600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
24	chr4:1165000-1166800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr4:1165000-1166800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr4:1165000-1167200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
27	chr4:1165200-1166200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:1165200-1166200	Flanking Active TSS	Esophagus	oesophagus
29	chr4:1165200-1166200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr4:1165200-1166200	Bivalent Enhancer	GM12878-XiMat	blood
31	chr4:1165200-1166400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
32	chr4:1165200-1166400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
33	chr4:1165200-1166400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:1165200-1166400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:1165200-1166400	Flanking Active TSS	Liver	Liver
36	chr4:1165200-1166400	Bivalent Enhancer	Stomach Mucosa	stomach
37	chr4:1165200-1166400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
38	chr4:1165200-1166600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr4:1165200-1166600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:1165200-1166600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:1165200-1166600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
42	chr4:1165200-1166600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:1165200-1166600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
44	chr4:1165200-1166600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
45	chr4:1165200-1166600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
46	chr4:1165200-1166800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr4:1165200-1167000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr4:1165200-1167000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr4:1165200-1167200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:1165200-1167200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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