Variant report

Variant	rs12407122
Chromosome Location	chr1:180420842-180420843
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10737342	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10798752	0.91[ASN][1000 genomes]
rs10798753	0.91[ASN][1000 genomes]
rs10798754	0.91[ASN][1000 genomes]
rs10798761	0.91[ASN][1000 genomes]
rs10798767	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10913969	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913970	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914002	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10914007	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12024156	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034669	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039933	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12045123	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045636	0.87[ASN][1000 genomes]
rs12085808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091722	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12142124	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12402815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12403665	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404209	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12405902	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12691484	0.91[ASN][1000 genomes]
rs1341924	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1418102	0.91[ASN][1000 genomes]
rs16856087	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1890731	0.91[ASN][1000 genomes]
rs28506072	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2877399	0.91[ASN][1000 genomes]
rs2877415	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737584	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806300	0.93[ASN][1000 genomes]
rs3806301	0.81[ASN][1000 genomes]
rs4424469	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4436345	0.91[ASN][1000 genomes]
rs4483365	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4543756	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4562579	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4593778	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4642852	0.91[ASN][1000 genomes]
rs4652495	0.90[ASN][1000 genomes]
rs4652496	0.91[ASN][1000 genomes]
rs4652498	0.91[ASN][1000 genomes]
rs4652499	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs55874160	0.91[ASN][1000 genomes]
rs60286873	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425625	0.91[ASN][1000 genomes]
rs6425634	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425641	0.81[ASN][1000 genomes]
rs6657492	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6659513	0.91[ASN][1000 genomes]
rs6661208	0.91[ASN][1000 genomes]
rs6678216	0.91[ASN][1000 genomes]
rs6680368	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6687442	0.81[ASN][1000 genomes]
rs6687549	0.81[ASN][1000 genomes]
rs72720915	0.91[ASN][1000 genomes]
rs72720917	0.91[ASN][1000 genomes]
rs7526189	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7538219	0.91[ASN][1000 genomes]
rs7538303	0.91[ASN][1000 genomes]
rs7539910	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7544585	0.91[ASN][1000 genomes]
rs822706	0.89[ASN][1000 genomes]
rs9701037	0.92[ASN][1000 genomes]
rs9726041	0.81[ASN][1000 genomes]
rs9729819	0.87[ASN][1000 genomes]
rs9730180	0.81[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	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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:180392600-180446200	Weak transcription	K562	blood
3	chr1:180401400-180430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:180403400-180426200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:180403400-180431200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:180403400-180448000	Weak transcription	HMEC	breast
7	chr1:180404000-180421800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:180404200-180431800	Weak transcription	NHEK	skin
9	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
10	chr1:180409200-180421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:180410000-180421200	Weak transcription	Ovary	ovary
12	chr1:180413000-180429400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:180417600-180431200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:180418000-180431200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:180418400-180422000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:180418400-180430800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:180418800-180422600	Weak transcription	Liver	Liver
18	chr1:180419000-180426200	Weak transcription	Dnd41	blood
19	chr1:180419400-180421600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr1:180419800-180422600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:180420000-180422200	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr1:180420000-180422400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:180420200-180421000	Strong transcription	Primary B cells from cord blood	blood
24	chr1:180420200-180421000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:180420200-180421000	ZNF genes & repeats	HSMM	muscle
26	chr1:180420200-180421200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:180420200-180421200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:180420200-180421200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr1:180420200-180421400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:180420200-180421600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr1:180420400-180421200	ZNF genes & repeats	GM12878-XiMat	blood
32	chr1:180420400-180421200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
33	chr1:180420400-180421400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
34	chr1:180420400-180421400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:180420600-180421000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:180420600-180421000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:180420600-180421000	ZNF genes & repeats	Brain Anterior Caudate	brain
38	chr1:180420600-180421000	ZNF genes & repeats	Fetal Brain Male	brain
39	chr1:180420600-180421000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
40	chr1:180420600-180421200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:180420600-180421200	ZNF genes & repeats	A549	lung
42	chr1:180420600-180421600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:180420600-180421600	ZNF genes & repeats	Fetal Brain Female	brain
44	chr1:180420600-180429600	Weak transcription	Fetal Lung	lung
45	chr1:180420800-180421000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:180420800-180421000	ZNF genes & repeats	Brain Substantia Nigra	brain
47	chr1:180420800-180421200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr1:180420800-180421200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
49	chr1:180420800-180422200	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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