Variant report

Variant	rs12615002
Chromosome Location	chr2:40621387-40621388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10865163	0.87[ASN][1000 genomes]
rs11124740	0.89[ASN][1000 genomes]
rs11886400	0.82[JPT][hapmap]
rs11890040	0.82[JPT][hapmap]
rs12465274	0.89[ASN][1000 genomes]
rs12472012	0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs12611557	0.86[ASN][1000 genomes]
rs17025877	0.82[JPT][hapmap]
rs34408472	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs56316253	0.83[ASN][1000 genomes]
rs57020706	0.87[ASN][1000 genomes]
rs6544331	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs7557545	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7570435	0.93[CHB][hapmap];0.91[CHD][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12615002	ABCG8	cis	parietal	SCAN
rs12615002	C2orf58	cis	parietal	SCAN
rs12615002	SLC8A1	cis	Whole Blood	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40601000-40621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:40608400-40622000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:40609600-40621800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:40612600-40622600	Weak transcription	HSMM	muscle
5	chr2:40617000-40621800	Weak transcription	Osteobl	bone
6	chr2:40617200-40623600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:40617600-40622800	Enhancers	Fetal Heart	heart
8	chr2:40619000-40624600	Weak transcription	Right Atrium	heart
9	chr2:40619800-40621600	Enhancers	Dnd41	blood
10	chr2:40620000-40622400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:40620200-40621400	Weak transcription	Fetal Brain Female	brain
12	chr2:40620200-40622000	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:40620800-40621400	Enhancers	Fetal Lung	lung
14	chr2:40620800-40622800	Enhancers	Primary B cells from cord blood	blood
15	chr2:40621000-40621400	Enhancers	Left Ventricle	heart
16	chr2:40621000-40622000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:40621000-40622200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr2:40621000-40622800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:40621000-40622800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:40621000-40623000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:40621000-40623000	Enhancers	Fetal Brain Male	brain
22	chr2:40621000-40623000	Enhancers	Placenta	Placenta
23	chr2:40621000-40623000	Enhancers	HMEC	breast
24	chr2:40621000-40624400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:40621200-40621400	Enhancers	Liver	Liver
26	chr2:40621200-40621400	Enhancers	Right Ventricle	heart
27	chr2:40621200-40622000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:40621200-40622600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:40621200-40623000	Enhancers	NHEK	skin
30	chr2:40621200-40624800	Enhancers	Placenta Amnion	Placenta Amnion

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