Variant report

Variant	rs9476837
Chromosome Location	chr6:15534270-15534271
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	POLR2A	chr6:15534209-15534312	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:15534139-15534500	GM12891	blood:	n/a	n/a
3	PBX3	chr6:15533928-15534289	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr6:15534220-15534370	GM12868	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15529195..15531595-chr6:15533933..15536941,3	K562	blood:

Variant related genes	Relation type
DTNBP1	TF binding region

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1018381	0.92[EUR][1000 genomes]
rs1018382	0.92[EUR][1000 genomes]
rs1040410	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10949305	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11752196	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11752598	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11753919	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755055	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11757499	0.89[EUR][1000 genomes]
rs11759609	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13437303	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876671	0.89[EUR][1000 genomes]
rs2205852	0.89[EUR][1000 genomes]
rs2237110	0.82[MEX][hapmap]
rs2619516	0.89[EUR][1000 genomes]
rs2619519	0.92[EUR][1000 genomes]
rs2619521	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2619522	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2619526	0.92[EUR][1000 genomes]
rs2619528	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2619529	0.89[EUR][1000 genomes]
rs2619530	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2619533	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2619534	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2619535	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2619540	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2619541	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2619544	0.92[EUR][1000 genomes]
rs2619545	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2619546	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2619548	0.89[EUR][1000 genomes]
rs2619552	0.88[EUR][1000 genomes]
rs2743548	0.89[EUR][1000 genomes]
rs2743549	0.89[EUR][1000 genomes]
rs2743550	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2743551	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2743552	0.89[EUR][1000 genomes]
rs2743553	0.89[EUR][1000 genomes]
rs2743853	0.89[EUR][1000 genomes]
rs2743854	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs2743857	1.00[JPT][hapmap]
rs2743858	0.92[EUR][1000 genomes]
rs2743859	0.92[EUR][1000 genomes]
rs2743860	0.92[EUR][1000 genomes]
rs2743861	1.00[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs2743864	0.92[EUR][1000 genomes]
rs2743865	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2743866	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2743867	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2743869	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2743870	0.92[EUR][1000 genomes]
rs2743871	0.92[EUR][1000 genomes]
rs2743872	0.92[EUR][1000 genomes]
rs3778651	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs734129	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs760761	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7752070	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7756793	0.85[CEU][hapmap]
rs7770921	0.89[EUR][1000 genomes]
rs875463	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296975	0.82[CEU][hapmap]
rs9296976	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9296977	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9296978	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296979	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296980	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9296981	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296984	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9296985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9296987	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9296988	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9464793	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9464794	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464795	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464797	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9464801	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9464802	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9464803	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs9464805	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9464807	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476835	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9476836	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9476838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9476839	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9476840	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9476841	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9476842	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9476844	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476845	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9476846	0.89[EUR][1000 genomes]
rs9476849	0.89[EUR][1000 genomes]
rs9476854	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9476858	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476859	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476860	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9476863	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes]
rs9476865	0.84[EUR][1000 genomes]
rs9476866	0.92[EUR][1000 genomes]
rs9476867	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476868	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9476869	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9476883	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv522265	chr6:15494177-15546213	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv428473	chr6:15522653-15595739	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15512600-15536400	Weak transcription	Psoas Muscle	Psoas
2	chr6:15523400-15534400	Weak transcription	HUVEC	blood vessel
3	chr6:15523600-15535800	Weak transcription	Small Intestine	intestine
4	chr6:15523600-15540000	Weak transcription	NHEK	skin
5	chr6:15524200-15535800	Weak transcription	Stomach Mucosa	stomach
6	chr6:15524400-15535400	Weak transcription	A549	lung
7	chr6:15524400-15549400	Weak transcription	Hela-S3	cervix
8	chr6:15524600-15536600	Weak transcription	Right Ventricle	heart
9	chr6:15524800-15536600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:15524800-15549800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:15525000-15536000	Weak transcription	NHLF	lung
12	chr6:15525000-15536400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:15525000-15536600	Weak transcription	Colonic Mucosa	Colon
14	chr6:15525000-15539000	Weak transcription	Brain Angular Gyrus	brain
15	chr6:15525000-15553400	Weak transcription	Ovary	ovary
16	chr6:15525200-15536400	Weak transcription	Adipose Nuclei	Adipose
17	chr6:15525400-15539000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:15527000-15535400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:15527200-15541400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:15528000-15534400	Strong transcription	Dnd41	blood
21	chr6:15528000-15534400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:15528400-15547400	Weak transcription	Fetal Kidney	kidney
23	chr6:15528600-15543600	Weak transcription	GM12878-XiMat	blood
24	chr6:15528600-15546800	Weak transcription	Fetal Lung	lung
25	chr6:15529000-15534400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:15529000-15534400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:15529000-15541200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:15529400-15535200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:15529400-15536400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:15529400-15549800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:15530000-15538800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr6:15530200-15534400	Strong transcription	Fetal Intestine Small	intestine
33	chr6:15530200-15536000	Weak transcription	Fetal Heart	heart
34	chr6:15530800-15534400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr6:15531000-15534400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:15531000-15536400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:15531200-15536200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:15531600-15534400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:15531600-15534400	Strong transcription	Primary T cells from cord blood	blood
40	chr6:15531600-15534600	Weak transcription	HSMMtube	muscle
41	chr6:15531800-15535400	Weak transcription	Liver	Liver
42	chr6:15531800-15536000	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:15531800-15536000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:15531800-15536600	Weak transcription	Left Ventricle	heart
45	chr6:15531800-15545800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:15532000-15535600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:15532000-15536000	Weak transcription	HepG2	liver
48	chr6:15532400-15536000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:15532400-15536400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:15532600-15535200	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links