Variant report

Variant	rs12073439
Chromosome Location	chr1:169284482-169284483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10047168	1.00[EUR][1000 genomes]
rs10800418	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10800430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800436	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs10800443	0.97[EUR][1000 genomes]
rs10800445	0.91[EUR][1000 genomes]
rs10919073	1.00[CEU][hapmap]
rs10919079	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919097	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919098	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10919100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];1.00[ASN][1000 genomes]
rs10919151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10919152	0.97[EUR][1000 genomes]
rs10919156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs1138486	1.00[CEU][hapmap]
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];1.00[ASN][1000 genomes]
rs11807896	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11810815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12058325	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12059944	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12061069	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12061080	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];0.97[ASN][1000 genomes]
rs12063719	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063863	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12067139	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12067351	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070031	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12071630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12074013	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12076519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079745	1.00[CEU][hapmap]
rs12080100	1.00[CHB][hapmap];1.00[JPT][hapmap]
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];0.89[ASN][1000 genomes]
rs12091133	0.91[EUR][1000 genomes]
rs12091844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][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];0.91[ASN][1000 genomes]
rs12097682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12561922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565852	0.91[EUR][1000 genomes]
rs1591734	0.82[ASN][1000 genomes]
rs2275300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs2280257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs2901092	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2982468	0.83[CHD][hapmap];1.00[MEX][hapmap]
rs3737683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3753298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3765227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3766052	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3766064	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3766077	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3766082	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3766088	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];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];1.00[ASN][1000 genomes]
rs60011235	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61806984	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7515326	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544446	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9628661	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]

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	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	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
3	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
4	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
5	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
6	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
8	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:169276800-169304600	Weak transcription	Ovary	ovary
10	chr1:169277000-169294600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:169278000-169285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:169279000-169288400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:169279000-169291200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:169279000-169293800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:169279000-169295600	Weak transcription	Adipose Nuclei	Adipose
17	chr1:169279200-169287200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:169279200-169296000	Weak transcription	Primary T cells from cord blood	blood
19	chr1:169280200-169304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:169281600-169294400	Weak transcription	Fetal Intestine Small	intestine
21	chr1:169281600-169294400	Weak transcription	Lung	lung
22	chr1:169281600-169306600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:169281800-169295400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:169282000-169285800	Weak transcription	HUVEC	blood vessel
25	chr1:169282000-169286000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:169282000-169288800	Weak transcription	A549	lung
27	chr1:169282000-169289600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:169282000-169290600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:169282000-169293800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:169282000-169294600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:169282000-169306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:169282200-169293600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:169282200-169295800	Weak transcription	NHEK	skin
34	chr1:169282400-169289200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:169282400-169295600	Weak transcription	NH-A	brain
36	chr1:169282800-169285800	Weak transcription	Hela-S3	cervix
37	chr1:169283000-169290400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:169283200-169287200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:169283400-169293400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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