Variant report

Variant	rs1553832
Chromosome Location	chr2:63013515-63013516
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10153716	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1022110	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11682530	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11688816	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11893131	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs12328837	0.93[JPT][hapmap]
rs12713467	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713468	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap]
rs12989754	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994674	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13013218	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1386399	0.87[JPT][hapmap]
rs1420018	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468748	0.92[CEU][hapmap]
rs1487074	0.93[JPT][hapmap]
rs1534418	0.87[JPT][hapmap]
rs1534420	0.87[JPT][hapmap]
rs17027429	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1828398	0.92[CEU][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1872789	0.87[JPT][hapmap]
rs1872790	0.93[JPT][hapmap]
rs189671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1906198	0.87[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs2058566	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058567	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2080227	0.81[CEU][hapmap]
rs2136737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.87[JPT][hapmap]
rs2215870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421816	0.87[CEU][hapmap]
rs2430388	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2539978	0.96[CEU][hapmap]
rs2539980	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2539985	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2539987	0.96[CEU][hapmap];0.94[CHB][hapmap]
rs2710637	0.83[CEU][hapmap]
rs2710638	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2710639	0.85[CEU][hapmap]
rs2710640	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2710642	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34104251	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs360797	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs360799	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360800	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360801	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs360804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360807	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360808	0.84[CHB][hapmap]
rs3927201	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671050	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4671051	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545968	0.93[JPT][hapmap]
rs6545969	0.93[JPT][hapmap]
rs6545971	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545972	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs6545973	0.87[CEU][hapmap]
rs6705835	0.93[JPT][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7562149	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7562734	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7567923	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7573756	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9678329	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9973612	0.96[CEU][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr2:62974200-63017200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:62982200-63033400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:63002200-63016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:63010600-63016000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:63010800-63014800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:63010800-63016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:63010800-63032800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:63011000-63014000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:63011000-63014000	Weak transcription	Fetal Stomach	stomach
10	chr2:63011000-63016600	Weak transcription	Pancreas	Pancrea
11	chr2:63011200-63016600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:63011600-63013600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:63011600-63014000	Enhancers	NHDF-Ad	bronchial
14	chr2:63011600-63014800	Enhancers	NHLF	lung
15	chr2:63011800-63014000	Enhancers	Osteobl	bone
16	chr2:63012000-63015000	Enhancers	NHEK	skin
17	chr2:63012000-63016000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:63012000-63018400	Enhancers	A549	lung
19	chr2:63012200-63013800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:63012200-63017800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:63012400-63013600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:63012400-63013600	Enhancers	Dnd41	blood
23	chr2:63012400-63013600	Enhancers	HMEC	breast
24	chr2:63012400-63013600	Enhancers	NH-A	brain
25	chr2:63012400-63015000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:63012400-63019400	Enhancers	Liver	Liver
27	chr2:63012800-63014200	Genic enhancers	HepG2	liver
28	chr2:63013000-63015000	Enhancers	Adipose Nuclei	Adipose
29	chr2:63013200-63013600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:63013200-63013600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr2:63013200-63014000	Enhancers	Stomach Smooth Muscle	stomach
32	chr2:63013200-63014200	Enhancers	Ovary	ovary
33	chr2:63013200-63015000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:63013200-63015000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:63013200-63015400	Enhancers	Colon Smooth Muscle	Colon
36	chr2:63013200-63015400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:63013200-63016600	Weak transcription	Right Atrium	heart
38	chr2:63013400-63014200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:63013400-63016200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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