Variant report

Variant	rs2799562
Chromosome Location	chr1:77755999-77756000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10747354	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1167207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1167215	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1167217	0.90[CEU][hapmap];0.89[CHB][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1177502	0.88[EUR][1000 genomes]
rs1377733	0.88[CHB][hapmap]
rs1463324	0.90[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17378915	0.82[AMR][1000 genomes]
rs1851736	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1988302	0.86[EUR][1000 genomes]
rs2602929	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602930	0.86[EUR][1000 genomes]
rs2602934	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs2602943	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2602945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2602946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2602948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602951	0.85[CEU][hapmap];0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602952	0.86[EUR][1000 genomes]
rs2689676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[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]
rs2799550	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2799554	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2799555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799556	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799558	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799559	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799560	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799561	0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799563	0.90[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815309	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815312	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2815314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815317	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2815324	0.90[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815325	0.90[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815326	0.90[CEU][hapmap];0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815327	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2815332	0.86[EUR][1000 genomes]
rs2815337	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6662853	0.90[CEU][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7531411	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs936001	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9439799	0.88[CHB][hapmap];0.92[ASN][1000 genomes]
rs9439819	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr1:77749000-77779200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:77749200-77778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:77749400-77781600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:77749800-77768800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:77750000-77757400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:77750600-77772400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:77750800-77768200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:77751000-77757400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:77751000-77767600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:77751200-77757800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:77751400-77764600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:77752200-77756400	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:77752600-77757200	Strong transcription	HSMM	muscle
14	chr1:77753400-77757600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:77754000-77757600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:77754400-77759600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:77754400-77785800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:77755000-77757000	Weak transcription	Brain Angular Gyrus	brain
19	chr1:77755000-77768800	Strong transcription	NHDF-Ad	bronchial
20	chr1:77755200-77756200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:77755200-77756600	Weak transcription	Primary T cells from cord blood	blood
22	chr1:77755200-77757600	Weak transcription	NHLF	lung
23	chr1:77755200-77781600	Weak transcription	Osteobl	bone
24	chr1:77755400-77757600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:77755400-77760800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:77755800-77788200	Weak transcription	HSMMtube	muscle

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