Variant report

Variant	rs9628661
Chromosome Location	chr1:169310283-169310284
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10047168	1.00[EUR][1000 genomes]
rs10800430	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800436	0.86[EUR][1000 genomes]
rs10800443	0.97[EUR][1000 genomes]
rs10800445	0.91[EUR][1000 genomes]
rs10919079	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919097	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919098	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919100	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919104	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919111	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919131	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919151	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10919152	0.97[EUR][1000 genomes]
rs10919156	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10919157	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10919159	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs11487548	0.91[EUR][1000 genomes]
rs11802239	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11805562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11807896	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810815	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12058325	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12059944	1.00[CEU][hapmap]
rs12061069	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12061080	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12061405	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12063056	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12063719	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063863	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12065030	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067139	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12070031	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12071630	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12073439	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12074013	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12076519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12081030	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs12081562	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12082748	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12083249	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12088672	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12091133	0.91[EUR][1000 genomes]
rs12091844	1.00[CEU][hapmap]
rs12092506	0.91[EUR][1000 genomes]
rs12092952	0.91[EUR][1000 genomes]
rs12094791	0.91[EUR][1000 genomes]
rs12097260	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12097682	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12561922	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565852	0.91[EUR][1000 genomes]
rs2275300	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs2280257	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs2901092	1.00[YRI][hapmap]
rs3737683	1.00[CEU][hapmap]
rs3753298	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3765227	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs3766052	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3766064	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3766082	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3766088	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766092	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820057	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41272453	0.91[EUR][1000 genomes]
rs57776592	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60011235	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61806984	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7515326	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544446	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
2	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
3	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:169291000-169313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:169296600-169310400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:169303000-169312600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:169303800-169317600	Weak transcription	Liver	Liver
10	chr1:169304800-169313200	Weak transcription	Spleen	Spleen
11	chr1:169305600-169312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
13	chr1:169306800-169310400	Weak transcription	Fetal Intestine Large	intestine
14	chr1:169307000-169310400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:169307000-169310400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:169308000-169311200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:169309400-169310800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:169309400-169314600	Weak transcription	K562	blood
20	chr1:169309400-169336400	Weak transcription	Ovary	ovary
21	chr1:169309800-169310600	Enhancers	Placenta Amnion	Placenta Amnion
22	chr1:169310000-169311600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:169310200-169310600	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:169310200-169310600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr1:169310200-169311000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:169310200-169311000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:169310200-169311000	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr1:169310200-169311200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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