Variant report

Variant	rs1534418
Chromosome Location	chr2:62883920-62883921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62883737..62887558-chr2:62889986..62892467,3	K562	blood:
2	chr2:62883289..62885199-chr2:62932148..62934917,2	K562	blood:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10172216	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10174703	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10177638	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10179232	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1038572	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs11125941	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11682530	0.93[JPT][hapmap]
rs11688816	0.86[JPT][hapmap]
rs11893614	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12328837	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12989754	0.87[JPT][hapmap]
rs13013218	0.81[JPT][hapmap]
rs13397831	0.84[EUR][1000 genomes]
rs13423306	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1386399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1386401	0.81[CEU][hapmap]
rs1487074	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1527959	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1534419	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553832	0.87[JPT][hapmap]
rs1830260	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1843778	0.87[AFR][1000 genomes]
rs1843779	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1872790	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs189671	0.87[JPT][hapmap]
rs2129509	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2136737	0.87[JPT][hapmap]
rs2204655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204656	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421713	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28814605	0.81[ASN][1000 genomes]
rs2901516	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs360799	0.87[JPT][hapmap]
rs360800	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs360801	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs360804	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs360807	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs4449117	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4461246	0.87[JPT][hapmap]
rs4479415	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4671050	0.93[JPT][hapmap]
rs6545965	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545966	0.83[ASN][1000 genomes]
rs6545967	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545969	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545971	0.86[JPT][hapmap]
rs6705835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6706506	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6727888	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749020	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6752010	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757128	0.92[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7349258	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7420881	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7421841	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573756	0.87[JPT][hapmap]
rs7587936	0.83[AFR][1000 genomes]
rs9678363	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9679110	0.83[ASN][1000 genomes]
rs974344	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs974345	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9752159	0.85[AFR][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	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62870400-62889600	Weak transcription	Right Atrium	heart
2	chr2:62881400-62885000	Weak transcription	Fetal Brain Male	brain
3	chr2:62881600-62885000	Enhancers	Liver	Liver
4	chr2:62881800-62886600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:62881800-62887200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:62882000-62892000	Weak transcription	Fetal Intestine Large	intestine
7	chr2:62882200-62886600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:62882200-62887200	Weak transcription	NH-A	brain
9	chr2:62882400-62886600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:62882400-62887000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:62882400-62888200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:62882400-62890000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:62882600-62886400	Weak transcription	NHEK	skin
14	chr2:62882600-62886600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:62882600-62886600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:62882600-62886800	Weak transcription	HSMM	muscle
17	chr2:62882600-62887000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:62882600-62887200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:62882600-62888200	Weak transcription	Esophagus	oesophagus
20	chr2:62882800-62886200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:62883000-62886000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:62883000-62886400	Weak transcription	HMEC	breast
23	chr2:62883000-62886600	Weak transcription	Osteobl	bone
24	chr2:62883600-62887200	Weak transcription	HepG2	liver

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