Variant report

Variant	rs12141929
Chromosome Location	chr1:77777898-77777899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10873935	1.00[YRI][hapmap]
rs11162318	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1167202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs1167212	1.00[CHB][hapmap];0.91[GIH][hapmap];0.97[EUR][1000 genomes]
rs12077763	1.00[CHD][hapmap]
rs12120921	1.00[CHD][hapmap]
rs12124822	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125503	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126330	0.84[EUR][1000 genomes]
rs12128049	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132273	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133976	1.00[CHB][hapmap]
rs12135843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140227	1.00[CEU][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]
rs1377737	1.00[CHB][hapmap]
rs1453981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17098287	1.00[CHB][hapmap]
rs17100458	1.00[CHB][hapmap]
rs17100463	1.00[CHB][hapmap]
rs17100476	1.00[CHB][hapmap]
rs17100509	1.00[YRI][hapmap]
rs17100513	1.00[YRI][hapmap]
rs2198511	1.00[YRI][hapmap]
rs2602937	1.00[YRI][hapmap]
rs2815307	1.00[YRI][hapmap]
rs4949773	1.00[CHD][hapmap]
rs4949788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap]
rs4949791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4949794	1.00[CHB][hapmap]
rs61096452	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61783074	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61784657	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546963	1.00[CHB][hapmap]
rs839828	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv3452343	chr1:77774348-77781734	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3452344	chr1:77774348-77781734	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv517088	chr1:77774413-77778608	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv818234	chr1:77774413-77778608	Weak transcription Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv2762157	chr1:77774413-77779836	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3692769	chr1:77774413-77781567	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	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
13	esv11859	chr1:77774744-77781454	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv441697	chr1:77774872-77779832	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv2756848	chr1:77775014-77788462	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv2758945	chr1:77775014-77788462	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 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	chr1:77754400-77785800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:77755200-77781600	Weak transcription	Osteobl	bone
6	chr1:77755800-77788200	Weak transcription	HSMMtube	muscle
7	chr1:77756800-77781600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:77758000-77778400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:77759000-77781600	Weak transcription	NHLF	lung
10	chr1:77771800-77780200	Strong transcription	NHDF-Ad	bronchial
11	chr1:77774000-77790400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:77774600-77778200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:77774600-77778600	Weak transcription	HSMM	muscle
14	chr1:77774600-77779200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:77774800-77778400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:77774800-77787200	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:77775200-77778400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:77776000-77778400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:77776000-77779000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:77776200-77779400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:77776600-77778000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr1:77776800-77779600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr1:77777000-77778000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:77777000-77778000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:77777000-77794600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:77777600-77778800	Enhancers	Primary T cells from cord blood	blood
27	chr1:77777800-77779200	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:77777800-77779400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:77777800-77780000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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