Variant report

Variant	rs12988659
Chromosome Location	chr2:40642626-40642627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10205556	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11685475	0.89[ASN][1000 genomes]
rs11901878	0.90[CHB][hapmap]
rs12052649	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12052650	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12052800	0.87[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12105764	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs13017237	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13023706	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031785	0.90[TSI][hapmap]
rs13031843	0.90[TSI][hapmap]
rs13031849	0.90[TSI][hapmap]
rs13035085	0.90[TSI][hapmap]
rs13414307	0.85[CHB][hapmap]
rs13418726	0.90[CHB][hapmap]
rs17025965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17025994	0.87[ASN][1000 genomes]
rs17026012	0.90[TSI][hapmap]
rs2888677	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2888678	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs34528721	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35129449	0.88[ASN][1000 genomes]
rs4366950	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4629203	0.81[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs4952621	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4952624	0.88[LWK][hapmap]
rs4993292	0.90[TSI][hapmap]
rs6712702	0.84[CHB][hapmap]
rs6737011	0.90[CHB][hapmap]
rs6742589	0.93[ASN][1000 genomes]
rs7579930	0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9789737	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9789739	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873916	chr2:40607504-40649084	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1007027	chr2:40627475-40649916	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40623600-40655000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40634800-40644800	Weak transcription	Left Ventricle	heart
3	chr2:40634800-40645800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:40635800-40643800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:40635800-40652600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:40636000-40645600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:40636200-40646000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:40637000-40645600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:40637200-40645600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:40637200-40646000	Weak transcription	Right Ventricle	heart
11	chr2:40637200-40649000	Weak transcription	Dnd41	blood
12	chr2:40637400-40643600	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:40639800-40643600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:40639800-40643600	Weak transcription	HMEC	breast
15	chr2:40639800-40643800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:40640000-40645600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:40640000-40645800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:40640000-40646600	Weak transcription	Osteobl	bone
19	chr2:40640000-40647600	Weak transcription	NHLF	lung
20	chr2:40640200-40643400	Weak transcription	NHEK	skin
21	chr2:40640200-40644800	Enhancers	Fetal Heart	heart
22	chr2:40640600-40642800	Strong transcription	HSMM	muscle
23	chr2:40641200-40647600	Weak transcription	Fetal Kidney	kidney
24	chr2:40642000-40642800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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