Variant report

Variant	rs12712643
Chromosome Location	chr2:39626388-39626389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39625232..39628414-chr2:39637317..39639794,4	K562	blood:
2	chr2:39624807..39627071-chr2:39638065..39639781,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1012689	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10175094	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs10185961	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs10193807	0.82[ASN][1000 genomes]
rs10865148	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs11124671	0.92[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs11124675	0.93[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs11124680	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11677383	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs11677611	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11688033	0.84[EUR][1000 genomes]
rs11695072	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs12151392	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12162306	0.84[ASN][1000 genomes]
rs12617901	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs12618944	0.81[ASN][1000 genomes]
rs12624242	0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs12712634	0.92[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs12712640	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712642	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1861733	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1861734	0.92[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap]
rs2024514	0.92[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap]
rs3755171	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs3755176	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs3770662	0.88[JPT][hapmap]
rs3770664	0.86[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3770671	0.92[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs3770672	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs3815594	0.88[ASW][hapmap];0.85[MEX][hapmap]
rs4670932	0.95[AFR][1000 genomes]
rs6544214	0.88[ASW][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs6709424	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs6714566	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs6755534	0.83[AFR][1000 genomes]
rs7340455	0.86[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7421175	0.88[EUR][1000 genomes]
rs7561630	0.81[ASN][1000 genomes]
rs7573923	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs7588265	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs7594145	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7598583	0.86[CHD][hapmap]
rs9037	0.92[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs9309036	0.83[GIH][hapmap];0.90[MEX][hapmap]
rs9309037	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
3	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
4	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:39609600-39626400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:39610200-39626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:39615800-39626800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:39616000-39626400	Weak transcription	Gastric	stomach
12	chr2:39617600-39626400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:39617800-39628200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:39617800-39628400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:39617800-39630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:39618000-39633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:39619200-39629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:39620000-39629400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:39620200-39635600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:39621800-39628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:39622000-39626400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:39622000-39626400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:39622000-39626400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:39622000-39626400	Weak transcription	Small Intestine	intestine
25	chr2:39622000-39626600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:39622000-39626600	Weak transcription	Pancreas	Pancrea
27	chr2:39622000-39628200	Weak transcription	Right Ventricle	heart
28	chr2:39622000-39628600	Weak transcription	Lung	lung
29	chr2:39622000-39635400	Weak transcription	HSMM	muscle
30	chr2:39622200-39626400	Weak transcription	Aorta	Aorta
31	chr2:39622400-39626400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:39622400-39626600	Weak transcription	NHLF	lung
33	chr2:39622600-39626400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:39622600-39626400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:39622600-39626400	Weak transcription	HSMMtube	muscle
36	chr2:39622600-39626400	Weak transcription	Osteobl	bone
37	chr2:39622600-39626800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:39622600-39643600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:39622800-39626400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:39622800-39626400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:39622800-39626400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:39622800-39626400	Weak transcription	Adipose Nuclei	Adipose
43	chr2:39622800-39626400	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:39622800-39626600	Weak transcription	Brain Angular Gyrus	brain
45	chr2:39622800-39626800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:39622800-39626800	Weak transcription	HMEC	breast
47	chr2:39622800-39630400	Weak transcription	Liver	Liver
48	chr2:39622800-39630400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:39622800-39630600	Weak transcription	Fetal Stomach	stomach
50	chr2:39622800-39643200	Weak transcription	Fetal Brain Male	brain

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