Variant report

Variant	rs3756915
Chromosome Location	chr6:100913012-100913013
allele	A/G
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	PBX3	chr6:100912578-100913243	SK-N-SH	brain:	n/a	chr6:100912908-100912917 chr6:100912876-100912885
2	TBP	chr6:100912832-100913325	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFYB	chr6:100912650-100913046	GM12878	blood:	n/a	chr6:100912873-100912888 chr6:100912906-100912920 chr6:100912908-100912918 chr6:100912905-100912920 chr6:100912909-100912921 chr6:100912905-100912920 chr6:100912874-100912888
4	POLR2A	chr6:100912824-100913234	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr6:100912890-100913255	ProgFib	skin:	n/a	n/a
6	SP1	chr6:100912614-100913150	H1-hESC	embryonic stem cell:	n/a	chr6:100912866-100912887 chr6:100912834-100912845
7	NFYB	chr6:100912652-100913091	K562	blood:	n/a	chr6:100912873-100912888 chr6:100912906-100912920 chr6:100912908-100912918 chr6:100912905-100912920 chr6:100912909-100912921 chr6:100912905-100912920 chr6:100912874-100912888
8	MAX	chr6:100912748-100913456	ECC-1	luminal epithelium:	n/a	chr6:100913325-100913334
9	TCF12	chr6:100912944-100913336	H1-hESC	embryonic stem cell:	n/a	n/a
10	SP4	chr6:100912701-100913110	H1-hESC	embryonic stem cell:	n/a	chr6:100912834-100912845
11	POLR2A	chr6:100912882-100916388	H1-neurons	neurons:	n/a	n/a
12	CHD2	chr6:100912685-100913316	H1-hESC	embryonic stem cell:	n/a	chr6:100912897-100912907
13	E2F6	chr6:100912548-100913422	H1-hESC	embryonic stem cell:	n/a	chr6:100912833-100912845
14	SP2	chr6:100912713-100913131	H1-hESC	embryonic stem cell:	n/a	chr6:100912875-100912885 chr6:100912907-100912917
15	SP2	chr6:100912658-100913133	H1-hESC	embryonic stem cell:	n/a	chr6:100912875-100912885 chr6:100912907-100912917
16	SP4	chr6:100912773-100913082	H1-hESC	embryonic stem cell:	n/a	chr6:100912834-100912845
17	MAX	chr6:100912766-100913332	ECC-1	luminal epithelium:	n/a	n/a
18	E2F6	chr6:100912625-100913299	H1-hESC	embryonic stem cell:	n/a	chr6:100912833-100912845
19	POLR2A	chr6:100912866-100913131	U87	brain:	n/a	n/a
20	POLR2A	chr6:100912732-100913230	HUVEC	blood vessel:	n/a	n/a
21	SUZ12	chr6:100910832-100914607	NT2-D1	testis:	n/a	n/a
22	SP1	chr6:100912723-100913069	GM12878	blood:	n/a	chr6:100912866-100912887 chr6:100912834-100912845
23	SUZ12	chr6:100912951-100915101	H1-hESC	embryonic stem cell:	n/a	n/a
24	PBX3	chr6:100912774-100913021	GM12878	blood:	n/a	chr6:100912908-100912917 chr6:100912876-100912885
25	ZNF263	chr6:100911621-100913246	HEK293-T-REx	kidney:	n/a	n/a
26	POLR2A	chr6:100912824-100913342	U87	brain:	n/a	n/a
27	MAX	chr6:100912687-100913350	H1-hESC	embryonic stem cell:	n/a	chr6:100913325-100913334
28	TAF1	chr6:100912735-100913298	ECC-1	luminal epithelium:	n/a	n/a
29	TAF1	chr6:100912713-100913204	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr6:100912818-100913348	U87	brain:	n/a	n/a
31	CTBP2	chr6:100912907-100913440	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr6:100912834-100913065	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr6:100912631-100913367	SK-N-MC	brain:	n/a	n/a
34	SP1	chr6:100912539-100913208	H1-hESC	embryonic stem cell:	n/a	chr6:100912866-100912887 chr6:100912834-100912845
35	PBX3	chr6:100912551-100913311	SK-N-SH	brain:	n/a	chr6:100912908-100912917 chr6:100912876-100912885
36	POLR2A	chr6:100912776-100916575	H1-neurons	neurons:	n/a	n/a
37	SIN3A	chr6:100912121-100913212	H1-hESC	embryonic stem cell:	n/a	chr6:100912349-100912358 chr6:100912451-100912462 chr6:100912451-100912464
38	KAP1	chr6:100912440-100913313	HEK293	kidney:	n/a	n/a
39	TCF12	chr6:100913002-100913399	ECC-1	luminal epithelium:	n/a	n/a
40	JUND	chr6:100912636-100913176	H1-hESC	embryonic stem cell:	n/a	chr6:100912875-100912884 chr6:100912907-100912916
41	TCF12	chr6:100912789-100913328	H1-hESC	embryonic stem cell:	n/a	n/a
42	ZNF143	chr6:100912780-100913211	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SIM1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12663321	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12663539	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17054156	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17060650	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17060652	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3798485	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56681764	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73496769	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73496776	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73496787	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7746426	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription 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	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100902000-100913600	Active TSS	Psoas Muscle	Psoas
2	chr6:100906600-100914200	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr6:100906800-100914400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:100906800-100914600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:100907400-100913600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:100908000-100913600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:100908000-100913800	Bivalent/Poised TSS	NHDF-Ad	bronchial
8	chr6:100908000-100914800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr6:100908400-100913800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:100908600-100913400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:100908600-100913400	Active TSS	HSMM	muscle
12	chr6:100908600-100913600	Active TSS	HSMMtube	muscle
13	chr6:100908800-100914000	Active TSS	Muscle Satellite Cultured Cells	--
14	chr6:100911000-100914400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr6:100911000-100914600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:100911200-100913400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
17	chr6:100911600-100913400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
18	chr6:100911800-100913200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:100911800-100913400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
20	chr6:100911800-100913400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:100911800-100913400	ZNF genes & repeats	Lung	lung
22	chr6:100911800-100913600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr6:100911800-100913600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr6:100911800-100913600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
25	chr6:100911800-100914200	ZNF genes & repeats	Spleen	Spleen
26	chr6:100911800-100916000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr6:100912000-100913200	Bivalent Enhancer	Fetal Thymus	thymus
28	chr6:100912000-100913400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr6:100912000-100913400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr6:100912000-100913400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
31	chr6:100912000-100913600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:100912000-100913600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
33	chr6:100912000-100913600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:100912000-100913800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:100912200-100913400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
36	chr6:100912200-100913400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
37	chr6:100912200-100913400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
38	chr6:100912200-100913400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
39	chr6:100912200-100913600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr6:100912200-100915800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:100912400-100913400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:100912400-100913400	Bivalent Enhancer	Fetal Brain Male	brain
43	chr6:100912400-100913400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
44	chr6:100912600-100913200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:100912600-100913200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
46	chr6:100912600-100913200	Bivalent Enhancer	Liver	Liver
47	chr6:100912600-100913200	Enhancers	Gastric	stomach
48	chr6:100912600-100913400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:100912600-100913400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
50	chr6:100912600-100913400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood

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