Variant report

Variant	rs3756790
Chromosome Location	chr6:75914009-75914010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:150)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:150 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:75914006-75914276	A549	lung:	n/a	n/a
2	POLR2A	chr6:75913829-75914276	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:75913976-75914272	Gliobla	brain:	n/a	n/a
4	CHD2	chr6:75913504-75914283	Hela-S3	cervix:	n/a	n/a
5	RFX5	chr6:75913466-75914332	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr6:75913877-75914304	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr6:75913862-75914329	MCF-7	breast:	n/a	n/a
8	RAD21	chr6:75913956-75914223	K562	blood:	n/a	n/a
9	RAD21	chr6:75913921-75914321	HepG2	liver:	n/a	n/a
10	SIN3A	chr6:75913935-75914305	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOXA1	chr6:75913985-75914207	T-47D	breast:	n/a	n/a
12	ZBTB33	chr6:75913778-75914291	HCT-116	colon:	n/a	n/a
13	E2F4	chr6:75913993-75914336	MCF10A-Er-Src	breast:	n/a	n/a
14	YY1	chr6:75913933-75914233	HCT-116	colon:	n/a	n/a
15	CHD2	chr6:75913880-75914145	HepG2	liver:	n/a	n/a
16	SMC3	chr6:75913424-75916272	Hela-S3	cervix:	n/a	n/a
17	GTF2F1	chr6:75913574-75914305	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr6:75913732-75914440	H1-hESC	embryonic stem cell:	n/a	n/a
19	SMC3	chr6:75913932-75914313	K562	blood:	n/a	n/a
20	CTCF	chr6:75914003-75914275	MCF-7	breast:	n/a	n/a
21	SUZ12	chr6:75913908-75917770	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr6:75913926-75914305	GM12878	blood:	n/a	n/a
23	MAZ	chr6:75913538-75917088	IMR90	lung:	n/a	chr6:75914516-75914523
24	CTCF	chr6:75913980-75914130	HL-60	blood:	n/a	n/a
25	CTCF	chr6:75914004-75914245	HepG2	liver:	n/a	n/a
26	CTCF	chr6:75913947-75914219	K562	blood:	n/a	n/a
27	CTCF	chr6:75913926-75914269	A549	lung:	n/a	n/a
28	SMARCC1	chr6:75913598-75916305	Hela-S3	cervix:	n/a	n/a
29	MAFK	chr6:75913982-75914165	HepG2	liver:	n/a	n/a
30	FOS	chr6:75913682-75914311	MCF10A-Er-Src	breast:	n/a	chr6:75914158-75914169
31	FOSL2	chr6:75913873-75914397	A549	lung:	n/a	n/a
32	FOSL2	chr6:75913968-75914246	HepG2	liver:	n/a	n/a
33	CTCF	chr6:75913986-75914215	ECC-1	luminal epithelium:	n/a	n/a
34	CTCF	chr6:75913990-75914287	MCF-7	breast:	n/a	n/a
35	JUND	chr6:75913923-75916368	H1-hESC	embryonic stem cell:	n/a	chr6:75915979-75915988 chr6:75914588-75914597
36	RCOR1	chr6:75913958-75914270	K562	blood:	n/a	n/a
37	RAD21	chr6:75913912-75914306	A549	lung:	n/a	n/a
38	CTCF	chr6:75913971-75914397	A549	lung:	n/a	n/a
39	CTCF	chr6:75913998-75914266	Hela-S3	cervix:	n/a	n/a
40	JUND	chr6:75913743-75914499	SK-N-SH	brain:	n/a	n/a
41	TCF7L2	chr6:75913564-75916132	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr6:75913993-75914206	HepG2	liver:	n/a	n/a
43	SUZ12	chr6:75913870-75918221	NT2-D1	testis:	n/a	n/a
44	YY1	chr6:75913954-75914243	GM12878	blood:	n/a	n/a
45	FOS	chr6:75913937-75914340	MCF10A-Er-Src	breast:	n/a	chr6:75914158-75914169
46	ZNF384	chr6:75913872-75914309	K562	blood:	n/a	n/a
47	RAD21	chr6:75913821-75914442	MCF-7	breast:	n/a	n/a
48	CTCF	chr6:75913982-75914259	Medullo	brain:	n/a	n/a
49	JUN	chr6:75914006-75914277	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr6:75913843-75914504	HCT-116	colon:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:75608999..75611267-chr6:75912636..75915418,2	MCF-7	breast:
2	chr6:74448984..74449504-chr6:75913700..75914546,2	K562	blood:
3	chr6:75609148..75609683-chr6:75913367..75914426,3	MCF-7	breast:
4	chr6:75649112..75649762-chr6:75913676..75914528,2	MCF-7	breast:
5	chr6:75912731..75914884-chr6:75919763..75921276,2	K562	blood:
6	chr6:75861359..75863350-chr6:75912949..75915219,2	MCF-7	breast:

No data

Variant related genes	Relation type
COL12A1	TF binding region
ENSG00000111799	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1203213	0.88[ASN][1000 genomes]
rs16886197	1.00[AMR][1000 genomes]
rs16886322	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16886323	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16886390	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs16886391	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1831689	0.91[ASN][1000 genomes]
rs2239642	1.00[AMR][1000 genomes]
rs2274901	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300791	0.84[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2300792	0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2300793	0.84[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2300794	1.00[AMR][1000 genomes]
rs240367	0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs240382	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs240400	0.83[ASN][1000 genomes]
rs240410	0.88[ASN][1000 genomes]
rs240424	0.89[ASN][1000 genomes]
rs240425	0.83[ASN][1000 genomes]
rs240431	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs240716	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240739	0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs240740	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34024604	0.92[ASN][1000 genomes]
rs3756789	0.84[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3777503	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545588	0.92[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs56705798	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57762746	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58104879	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58259480	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59338586	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59681030	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs598034	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs601008	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60309896	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60808683	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60891734	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs612266	0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61293108	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658592	0.88[ASN][1000 genomes]
rs6906960	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73463837	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463838	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463840	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463847	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463851	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463852	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463855	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463859	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463862	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463865	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463868	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463869	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463875	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463878	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463879	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463881	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463884	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463885	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463887	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463888	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463889	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73463890	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463895	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463897	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463898	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463899	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463900	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73463901	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73465805	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467620	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467622	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467625	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467626	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467628	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467636	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467639	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467641	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467644	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467651	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467652	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467656	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73467659	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs743004	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022377	chr6:75762463-75919592	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv538309	chr6:75762463-75919592	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830697	chr6:75763095-75915029	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv886181	chr6:75852488-75919484	Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
11	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75908400-75915400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:75911800-75916400	Active TSS	HSMMtube	muscle
3	chr6:75912200-75914200	Weak transcription	Aorta	Aorta
4	chr6:75912200-75914200	Weak transcription	Esophagus	oesophagus
5	chr6:75912200-75914200	Weak transcription	Pancreas	Pancrea
6	chr6:75912400-75914200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:75912600-75914200	Weak transcription	Lung	lung
8	chr6:75912600-75915000	Weak transcription	Gastric	stomach
9	chr6:75912800-75914200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:75912800-75914200	Active TSS	Fetal Muscle Trunk	muscle
11	chr6:75912800-75916200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:75912800-75916600	Active TSS	Ovary	ovary
13	chr6:75913000-75914600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:75913000-75915000	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:75913000-75916600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:75913000-75918400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:75913200-75916400	Active TSS	NHLF	lung
18	chr6:75913400-75914400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr6:75913400-75914400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
20	chr6:75913400-75916600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr6:75913600-75914200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:75913600-75914200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
23	chr6:75913600-75914200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
24	chr6:75913600-75914200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
25	chr6:75913600-75914200	Enhancers	HUVEC	blood vessel
26	chr6:75913600-75916600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
27	chr6:75913600-75917200	Active TSS	NHDF-Ad	bronchial
28	chr6:75913600-75917400	Bivalent/Poised TSS	Fetal Kidney	kidney
29	chr6:75913600-75918400	Active TSS	Rectal Smooth Muscle	rectum
30	chr6:75913800-75914200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
31	chr6:75913800-75914200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr6:75913800-75914200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:75913800-75914200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
34	chr6:75913800-75914200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:75913800-75914200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr6:75913800-75914200	Bivalent Enhancer	Brain Substantia Nigra	brain
37	chr6:75913800-75914200	Bivalent/Poised TSS	Fetal Brain Female	brain
38	chr6:75913800-75914200	Bivalent Enhancer	Fetal Heart	heart
39	chr6:75913800-75914200	Bivalent Enhancer	Stomach Mucosa	stomach
40	chr6:75913800-75914400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:75913800-75914400	Active TSS	Psoas Muscle	Psoas
42	chr6:75913800-75914800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
43	chr6:75913800-75914800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:75913800-75914800	Active TSS	A549	lung
45	chr6:75913800-75915000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:75913800-75915000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:75913800-75915200	Bivalent Enhancer	Liver	Liver
48	chr6:75913800-75915200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
49	chr6:75913800-75915400	Active TSS	Right Ventricle	heart
50	chr6:75913800-75916000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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