Variant report

Variant	rs7871477
Chromosome Location	chr9:21810531-21810532
allele	G/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	POLR2A	chr9:21810447-21810612	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:21810458-21811040	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:21810371-21811333	MCF-7	breast:	n/a	n/a
4	RUNX3	chr9:21810383-21810845	GM12878	blood:	n/a	n/a
5	EBF1	chr9:21810367-21810670	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:21810379-21810658	HCT-116	colon:	n/a	n/a
7	POLR2A	chr9:21810498-21810897	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000266732	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10217131	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217379	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10429489	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10511700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10757256	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10811609	0.80[ASN][1000 genomes]
rs10811616	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10811619	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10811624	0.81[CEU][hapmap]
rs10811631	0.85[JPT][hapmap]
rs10965124	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10965131	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10965150	0.81[CEU][hapmap]
rs10965157	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10965158	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12002238	0.84[ASN][1000 genomes]
rs12002663	0.90[ASN][1000 genomes]
rs12004745	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12336678	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12336734	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12337510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12340988	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12348845	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12378675	0.80[CEU][hapmap]
rs12379110	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12380313	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12380373	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13286524	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13302653	0.91[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1414258	0.85[ASN][1000 genomes]
rs1414259	0.85[ASN][1000 genomes]
rs1440992	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1544195	0.81[CEU][hapmap]
rs2039971	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2282245	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35235093	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35526535	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3931609	0.91[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4295749	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4326466	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4375086	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4399022	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4543632	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs55656405	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56005066	0.84[ASN][1000 genomes]
rs56237731	0.83[ASN][1000 genomes]
rs56339876	0.83[ASN][1000 genomes]
rs58495931	0.84[ASN][1000 genomes]
rs59990401	0.86[ASN][1000 genomes]
rs61258965	0.84[ASN][1000 genomes]
rs6475575	0.85[ASN][1000 genomes]
rs6475580	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475581	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475582	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6475583	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6475584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475588	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6475589	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66506556	0.81[ASN][1000 genomes]
rs66587337	0.85[ASN][1000 genomes]
rs67220270	0.81[ASN][1000 genomes]
rs7022981	0.81[ASN][1000 genomes]
rs7029287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7033148	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7040432	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7040895	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7041509	0.88[EUR][1000 genomes]
rs7042728	0.91[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7042884	0.85[ASN][1000 genomes]
rs7850447	0.81[ASN][1000 genomes]
rs7851125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859886	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860126	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866362	0.85[ASN][1000 genomes]
rs7866533	0.85[ASN][1000 genomes]
rs7866860	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7867176	1.00[CEU][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7868246	0.82[ASN][1000 genomes]
rs7868253	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7869680	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7871631	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7874112	0.91[CEU][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs885518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298826	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs935054	0.81[ASN][1000 genomes]
rs945263	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21810800	Weak transcription	Right Ventricle	heart
2	chr9:21804000-21814200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:21804000-21817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:21804200-21810800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:21804200-21813200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:21804200-21813200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:21804400-21813200	Weak transcription	Colonic Mucosa	Colon
9	chr9:21804400-21816000	Weak transcription	Fetal Kidney	kidney
10	chr9:21804800-21813600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:21805000-21810800	Weak transcription	Brain Anterior Caudate	brain
12	chr9:21805000-21811200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:21805000-21812000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:21805000-21813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:21805000-21816200	Weak transcription	Fetal Brain Male	brain
16	chr9:21805200-21810800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr9:21805200-21810800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:21805200-21812800	Strong transcription	Fetal Stomach	stomach
19	chr9:21805200-21813200	Weak transcription	Psoas Muscle	Psoas
20	chr9:21805200-21813400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:21805400-21812600	Strong transcription	Fetal Intestine Large	intestine
22	chr9:21805800-21813200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:21805800-21813200	Weak transcription	Brain Angular Gyrus	brain
24	chr9:21806000-21812400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:21806000-21812600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:21806000-21817600	Genic enhancers	HMEC	breast
27	chr9:21806200-21813200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr9:21806400-21812200	Strong transcription	Fetal Intestine Small	intestine
29	chr9:21806400-21812400	Strong transcription	HepG2	liver
30	chr9:21806400-21812800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:21806400-21813200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr9:21806400-21813200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:21806400-21819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:21806600-21810800	Weak transcription	Pancreas	Pancrea
35	chr9:21806600-21812200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr9:21806600-21812400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:21806600-21815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr9:21806800-21810800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:21806800-21810800	Weak transcription	Lung	lung
41	chr9:21806800-21811600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:21806800-21812000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:21806800-21812000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:21806800-21812800	Strong transcription	Primary T cells from cord blood	blood
45	chr9:21806800-21813200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:21806800-21815800	Weak transcription	Brain Germinal Matrix	brain
47	chr9:21807000-21812000	Strong transcription	Fetal Muscle Leg	muscle
48	chr9:21807000-21813600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:21807200-21810800	Weak transcription	Gastric	stomach
50	chr9:21807200-21811400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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