Variant report

Variant	rs9457187
Chromosome Location	chr6:167000602-167000603
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	SP1	chr6:167000139-167000802	HCT-116	colon:	n/a	n/a
2	NFE2	chr6:167000249-167000616	GM12878	blood:	n/a	n/a
3	SP1	chr6:167000199-167000646	GM12878	blood:	n/a	n/a
4	USF2	chr6:167000238-167000622	H1-hESC	embryonic stem cell:	n/a	chr6:167000428-167000439
5	YY1	chr6:167000217-167000616	ECC-1	luminal epithelium:	n/a	n/a
6	USF1	chr6:167000166-167000747	ECC-1	luminal epithelium:	n/a	chr6:167000427-167000438
7	ZNF143	chr6:167000197-167000619	K562	blood:	n/a	n/a
8	IRF3	chr6:167000290-167000616	GM12878	blood:	n/a	n/a
9	USF1	chr6:167000185-167000815	HCT-116	colon:	n/a	chr6:167000427-167000438
10	NFYB	chr6:167000237-167000868	Hela-S3	cervix:	n/a	chr6:167000440-167000455
11	CREB1	chr6:167000296-167000639	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr6:167000039-167000839	HCT-116	colon:	n/a	n/a
13	USF2	chr6:167000261-167000623	Hela-S3	cervix:	n/a	chr6:167000428-167000439
14	SP1	chr6:167000280-167000647	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF143	chr6:167000206-167000637	H1-hESC	embryonic stem cell:	n/a	n/a
16	SP1	chr6:167000174-167000668	A549	lung:	n/a	n/a
17	FOS	chr6:167000265-167000631	K562	blood:	n/a	n/a
18	USF1	chr6:167000204-167000621	A549	lung:	n/a	chr6:167000427-167000438
19	POLR2A	chr6:167000381-167003269	GM12891	blood:	n/a	n/a
20	USF1	chr6:167000290-167000606	A549	lung:	n/a	chr6:167000427-167000438
21	YY1	chr6:167000235-167000606	GM12878	blood:	n/a	n/a
22	CHD2	chr6:167000282-167000605	GM12878	blood:	n/a	n/a
23	SIX5	chr6:167000150-167000616	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:167000300-167002507	Raji	blood:	n/a	n/a
25	SIX5	chr6:167000270-167000607	K562	blood:	n/a	n/a
26	NFYB	chr6:167000208-167000908	K562	blood:	n/a	chr6:167000440-167000455
27	YY1	chr6:167000245-167000614	ECC-1	luminal epithelium:	n/a	n/a
28	MAX	chr6:167000272-167000602	GM12878	blood:	n/a	n/a
29	ETS1	chr6:167000226-167000616	K562	blood:	n/a	n/a
30	NFYA	chr6:167000253-167000615	K562	blood:	n/a	n/a
31	USF1	chr6:167000231-167000604	H1-hESC	embryonic stem cell:	n/a	chr6:167000427-167000438
32	WRNIP1	chr6:167000316-167000819	GM12878	blood:	n/a	n/a
33	HCFC1	chr6:167000211-167000730	K562	blood:	n/a	n/a
34	USF1	chr6:167000238-167000607	SK-N-SH_RA	brain:	n/a	chr6:167000427-167000438
35	ZEB1	chr6:167000287-167000637	GM12878	blood:	n/a	chr6:167000420-167000429
36	NFYB	chr6:167000140-167000957	GM12878	blood:	n/a	chr6:167000440-167000455
37	USF1	chr6:167000129-167000848	HCT-116	colon:	n/a	chr6:167000427-167000438
38	USF1	chr6:167000149-167000687	ECC-1	luminal epithelium:	n/a	chr6:167000427-167000438
39	HCFC1	chr6:167000253-167000710	Hela-S3	cervix:	n/a	n/a
40	SP1	chr6:167000133-167000674	A549	lung:	n/a	n/a
41	SIX5	chr6:167000131-167000609	GM12878	blood:	n/a	n/a
42	USF1	chr6:167000166-167000652	K562	blood:	n/a	chr6:167000427-167000438
43	NFYA	chr6:167000215-167000653	GM12878	blood:	n/a	n/a
44	USF1	chr6:167000127-167000672	SK-N-SH	brain:	n/a	chr6:167000427-167000438
45	USF1	chr6:167000156-167000696	SK-N-SH	brain:	n/a	chr6:167000427-167000438
46	SP1	chr6:167000215-167000632	GM12878	blood:	n/a	n/a
47	ZNF143	chr6:167000199-167000638	GM12878	blood:	n/a	n/a
48	CHD2	chr6:167000293-167000620	K562	blood:	n/a	n/a
49	USF2	chr6:167000227-167000632	GM12878	blood:	n/a	chr6:167000428-167000439
50	SP1	chr6:167000272-167000690	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
FAM103A2P	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10214670	0.86[JPT][hapmap]
rs12190451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778382	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778384	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778386	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778390	0.86[EUR][1000 genomes]
rs3778391	0.86[EUR][1000 genomes]
rs3799584	0.90[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs3799597	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799598	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799600	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799602	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799603	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799607	0.86[EUR][1000 genomes]
rs4710069	0.95[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4710070	0.95[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs4710071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56064314	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6928849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742514	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295353	0.95[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs9457189	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv5592	chr6:166958317-167002951	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	esv3522272	chr6:166998312-167001210	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2580547	chr6:166998381-167000738	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv3522269	chr6:166998589-167000640	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166981800-167002400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:166986200-167002200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:166986600-167001400	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:166986800-167003000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:166987000-167002000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:166987200-167001800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:166989000-167011400	Weak transcription	Ovary	ovary
8	chr6:166989600-167001800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:166990600-167001800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:166993600-167003000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:166993800-167001800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:166994000-167003600	Weak transcription	Brain Germinal Matrix	brain
13	chr6:166994800-167002000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:166995600-167002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:166995800-167001200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:166995800-167001600	Weak transcription	Gastric	stomach
18	chr6:166995800-167002200	Weak transcription	Right Ventricle	heart
19	chr6:166996800-167001400	Weak transcription	Brain Anterior Caudate	brain
20	chr6:166997000-167002200	Weak transcription	Pancreas	Pancrea
21	chr6:166997000-167003000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:166997200-167002000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:166997200-167002200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:166997200-167003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:166997200-167006000	Weak transcription	Aorta	Aorta
26	chr6:166997400-167003000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:166997600-167002200	Weak transcription	HMEC	breast
28	chr6:166997800-167001200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:166997800-167001600	Weak transcription	Lung	lung
30	chr6:166998000-167000800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:166998200-167002200	Weak transcription	Left Ventricle	heart
33	chr6:166998600-167001400	Weak transcription	Fetal Stomach	stomach
34	chr6:166998600-167002400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:166998800-167001200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:166998800-167001200	Weak transcription	NH-A	brain
37	chr6:166998800-167001400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:166998800-167001800	Weak transcription	Right Atrium	heart
39	chr6:166998800-167001800	Weak transcription	HSMMtube	muscle
40	chr6:166998800-167002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:166998800-167002200	Weak transcription	NHLF	lung
42	chr6:166998800-167004000	Weak transcription	Fetal Brain Male	brain
43	chr6:166999000-167000800	Weak transcription	Fetal Heart	heart
44	chr6:166999000-167001600	Weak transcription	HSMM	muscle
45	chr6:166999000-167002000	Weak transcription	Osteobl	bone
46	chr6:166999000-167002200	Weak transcription	NHDF-Ad	bronchial
47	chr6:166999800-167004000	Enhancers	Fetal Thymus	thymus
48	chr6:167000000-167000800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:167000000-167003000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr6:167000000-167003400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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