Variant report

Variant	rs12404209
Chromosome Location	chr1:180415151-180415152
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180405935..180408153-chr1:180413582..180416422,2	K562	blood:
2	chr1:180412644..180415176-chr1:180424963..180427145,2	MCF-7	breast:
3	chr1:180414436..180416296-chr1:180466965..180469028,2	K562	blood:
4	chr1:180211506..180213234-chr1:180414919..180417666,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265435	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10494525	1.00[CEU][hapmap]
rs10737342	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10753209	0.80[CHB][hapmap]
rs10753211	0.82[CHB][hapmap]
rs10798745	0.86[CHB][hapmap]
rs10798746	0.82[CHB][hapmap]
rs10798752	0.89[ASN][1000 genomes]
rs10798753	0.89[ASN][1000 genomes]
rs10798754	0.89[ASN][1000 genomes]
rs10798759	0.81[CHB][hapmap]
rs10798761	0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10798762	0.81[CHB][hapmap]
rs10798767	0.91[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs10913969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913970	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913980	0.81[CHB][hapmap]
rs10913981	0.82[CHB][hapmap]
rs10913984	0.82[CHB][hapmap]
rs10913985	0.81[CHB][hapmap]
rs10913994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10914002	0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10914007	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10914017	0.80[CHB][hapmap]
rs11580793	0.82[CHB][hapmap]
rs12024156	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12034217	0.82[CHB][hapmap]
rs12034669	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039331	0.90[JPT][hapmap]
rs12039933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045123	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12045636	0.85[ASN][1000 genomes]
rs12085808	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12091722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12140076	1.00[YRI][hapmap]
rs12142124	0.91[ASN][1000 genomes]
rs12402815	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403665	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12405902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12407122	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12691484	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12730889	0.82[CHB][hapmap]
rs1341924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1416823	0.90[CHB][hapmap]
rs1418102	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1538620	0.81[CHB][hapmap]
rs1575710	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs16856087	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1890731	0.89[ASN][1000 genomes]
rs1925339	0.81[CHB][hapmap]
rs2296378	0.81[CHB][hapmap]
rs28506072	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2877399	0.89[ASN][1000 genomes]
rs2877415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3737584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806300	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3806301	0.85[CHB][hapmap]
rs4058058	0.81[CHB][hapmap]
rs4076403	0.81[CHB][hapmap]
rs4421553	0.82[CHB][hapmap]
rs4424469	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs4436345	0.89[ASN][1000 genomes]
rs4483365	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4543756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4562579	0.91[ASN][1000 genomes]
rs4578179	0.81[CHB][hapmap]
rs4593778	0.91[ASN][1000 genomes]
rs4642852	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4651064	0.82[CHB][hapmap]
rs4652495	0.88[ASN][1000 genomes]
rs4652496	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4652498	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4652499	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4652505	0.81[CHB][hapmap]
rs55874160	0.89[ASN][1000 genomes]
rs60286873	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425625	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6425634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425644	0.86[JPT][hapmap]
rs6657492	0.89[ASN][1000 genomes]
rs6659513	0.89[ASN][1000 genomes]
rs6661208	0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6665719	0.82[CHB][hapmap]
rs6670544	0.82[CHB][hapmap]
rs6678216	0.89[ASN][1000 genomes]
rs6680368	0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs6699076	0.90[JPT][hapmap]
rs6704334	0.89[CHB][hapmap]
rs6704437	0.90[CHB][hapmap]
rs72720915	0.89[ASN][1000 genomes]
rs72720917	0.89[ASN][1000 genomes]
rs7519288	1.00[CEU][hapmap]
rs7526189	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528650	0.81[CHB][hapmap]
rs7538219	0.89[ASN][1000 genomes]
rs7538303	0.89[ASN][1000 genomes]
rs7539910	0.91[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs7544585	0.89[ASN][1000 genomes]
rs822706	0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs9701037	0.90[ASN][1000 genomes]
rs9726041	0.90[CHB][hapmap]
rs9729819	0.85[ASN][1000 genomes]
rs9730180	0.90[CHB][hapmap]

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	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180365200-180420600	Weak transcription	A549	lung
2	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:180392600-180446200	Weak transcription	K562	blood
4	chr1:180394800-180420200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:180399000-180420800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:180399600-180420400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:180399600-180420400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:180401400-180420200	Weak transcription	HSMM	muscle
9	chr1:180401400-180430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:180401800-180420800	Weak transcription	NHDF-Ad	bronchial
11	chr1:180403400-180426200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:180403400-180431200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:180403400-180448000	Weak transcription	HMEC	breast
14	chr1:180404000-180421800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:180404200-180431800	Weak transcription	NHEK	skin
16	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
17	chr1:180406200-180420200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:180406600-180420600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:180409200-180421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:180410000-180421200	Weak transcription	Ovary	ovary
21	chr1:180411600-180419400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:180411600-180420200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:180411600-180420800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:180412600-180420000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:180413000-180429400	Weak transcription	Fetal Intestine Small	intestine
26	chr1:180413600-180419400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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