Variant report

Variant	rs12712640
Chromosome Location	chr2:39604876-39604877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
2	chr2:39604271..39606896-chr2:39836073..39838950,2	K562	blood:
3	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:
4	chr2:39596692..39599194-chr2:39603552..39605779,2	K562	blood:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1012689	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10175094	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10185961	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10193807	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10196407	0.84[CHB][hapmap]
rs10865148	0.93[ASW][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11124671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11124675	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11124680	0.85[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11677383	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11677611	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11688033	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11688352	0.83[ASN][1000 genomes]
rs11689327	0.83[AMR][1000 genomes]
rs11695072	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs12151392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12162306	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12617901	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs12618944	0.87[ASN][1000 genomes]
rs12624242	0.92[ASW][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.88[ASN][1000 genomes]
rs12712634	0.93[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12712642	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712643	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13405577	0.80[ASN][1000 genomes]
rs13425432	0.82[JPT][hapmap]
rs1861733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1861734	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2024514	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2058863	0.81[AMR][1000 genomes]
rs2302749	0.81[ASN][1000 genomes]
rs2373530	0.86[ASW][hapmap]
rs3755171	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3755172	0.85[ASN][1000 genomes]
rs3755176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3770662	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3770663	0.86[ASW][hapmap];0.81[MEX][hapmap]
rs3770664	0.86[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3770671	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs3770672	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770673	0.81[ASN][1000 genomes]
rs3770674	0.80[ASN][1000 genomes]
rs3815594	0.81[MEX][hapmap]
rs4670938	0.89[MKK][hapmap]
rs6544214	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs6544215	0.85[ASN][1000 genomes]
rs6544216	0.81[ASN][1000 genomes]
rs6709424	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6714566	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6719469	0.81[ASN][1000 genomes]
rs6720537	0.88[MKK][hapmap]
rs6720951	0.86[ASW][hapmap];0.89[MKK][hapmap]
rs6743345	0.84[CHB][hapmap]
rs6753014	0.81[ASN][1000 genomes]
rs6758596	0.90[MKK][hapmap]
rs7340455	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7421175	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7561630	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7569037	0.87[ASN][1000 genomes]
rs7573923	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7581692	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7582848	0.81[ASN][1000 genomes]
rs7594145	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7596222	0.93[ASW][hapmap];0.82[LWK][hapmap]
rs7597300	0.83[ASN][1000 genomes]
rs7598583	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs7603337	0.85[ASN][1000 genomes]
rs7605427	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7605939	0.92[MKK][hapmap]
rs7608958	0.81[ASN][1000 genomes]
rs9037	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.85[ASN][1000 genomes]
rs9309036	0.93[ASW][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9309037	0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9309038	0.81[AMR][1000 genomes]
rs9309039	0.81[AMR][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	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
2	chr2:39588000-39607800	Weak transcription	Ovary	ovary
3	chr2:39588000-39608800	Weak transcription	Lung	lung
4	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
6	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:39592000-39606800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:39592600-39607000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:39594600-39608800	Weak transcription	Left Ventricle	heart
11	chr2:39595800-39606800	Weak transcription	HUVEC	blood vessel
12	chr2:39595800-39607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:39596200-39605000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:39596400-39605000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:39596400-39606800	Weak transcription	Fetal Brain Male	brain
16	chr2:39596800-39605600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:39597200-39607800	Weak transcription	Small Intestine	intestine
18	chr2:39597600-39605600	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:39597600-39606200	Weak transcription	Brain Anterior Caudate	brain
20	chr2:39597600-39606200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:39598600-39606400	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:39600000-39606400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:39600600-39606800	Weak transcription	Fetal Kidney	kidney
24	chr2:39600600-39614600	Weak transcription	Aorta	Aorta
25	chr2:39600800-39606200	Weak transcription	Brain Substantia Nigra	brain
26	chr2:39601000-39605000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:39601000-39606800	Weak transcription	NHEK	skin
28	chr2:39601200-39606200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:39601400-39607000	Weak transcription	Fetal Brain Female	brain
30	chr2:39601600-39609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr2:39601800-39606800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:39602800-39605600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:39603000-39606800	Weak transcription	Fetal Stomach	stomach
34	chr2:39603200-39605800	Weak transcription	Adipose Nuclei	Adipose
35	chr2:39603200-39606800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:39603200-39606800	Weak transcription	A549	lung
37	chr2:39603200-39608200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:39603200-39609000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
40	chr2:39603400-39605000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:39603400-39605400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:39603400-39606600	Weak transcription	NHDF-Ad	bronchial
43	chr2:39603400-39607800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:39603400-39612000	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:39603400-39613200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
48	chr2:39603600-39607800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:39603800-39606200	Weak transcription	Liver	Liver
50	chr2:39603800-39606400	Weak transcription	Dnd41	blood

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