Variant report

Variant	rs2602934
Chromosome Location	chr1:77822740-77822741
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10747354	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1167207	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs1167215	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1167217	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1177502	0.81[EUR][1000 genomes]
rs1377733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1377734	0.98[ASN][1000 genomes]
rs1463324	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1851736	0.82[CEU][hapmap]
rs2602929	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602943	0.81[CHB][hapmap]
rs2602945	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs2602946	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs2602948	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs2602951	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2689676	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes]
rs2689683	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs2799550	0.84[ASN][1000 genomes]
rs2799554	0.84[ASN][1000 genomes]
rs2799555	0.85[CEU][hapmap];0.88[CHB][hapmap]
rs2799562	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs2799563	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2815314	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs2815317	0.81[CHB][hapmap]
rs2815319	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2815324	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2815325	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2815326	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2815327	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2815337	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6662853	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7531411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs936001	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9439799	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9439819	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77789000-77831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:77795000-77836400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:77801000-77825800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:77803400-77839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:77813800-77834200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:77814400-77835600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:77816000-77824000	Weak transcription	Brain Anterior Caudate	brain
8	chr1:77816200-77825800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:77817400-77834200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:77819800-77826800	Weak transcription	NHDF-Ad	bronchial
11	chr1:77819800-77835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:77820200-77823600	Weak transcription	Fetal Brain Male	brain
13	chr1:77820400-77823400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:77820400-77836400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:77821000-77825600	Weak transcription	HSMMtube	muscle
16	chr1:77821000-77835600	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:77821400-77825400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:77821400-77825600	Weak transcription	HSMM	muscle
19	chr1:77822200-77822800	Enhancers	Brain Substantia Nigra	brain
20	chr1:77822400-77823800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:77822600-77825600	Weak transcription	Brain Cingulate Gyrus	brain

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