Variant report

Variant	rs7964860
Chromosome Location	chr12:66702158-66702159
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10748038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10748039	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784521	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10784523	0.87[AFR][1000 genomes]
rs10784524	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10878403	0.86[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs11176137	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11176138	0.88[CEU][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11176139	0.94[EUR][1000 genomes]
rs11176142	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs11176144	0.88[EUR][1000 genomes]
rs12367438	0.89[EUR][1000 genomes]
rs12816200	0.89[EUR][1000 genomes]
rs1495495	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1898305	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118139	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3741603	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4382951	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4430553	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4554930	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581676	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7131920	0.87[AFR][1000 genomes]
rs7132724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7133479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7298868	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7315366	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7316880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7956960	0.99[EUR][1000 genomes]
rs7957877	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7959466	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969887	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973358	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7964860	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66696800-66703800	Weak transcription	Lung	lung
2	chr12:66696800-66714800	Weak transcription	NHDF-Ad	bronchial
3	chr12:66696800-66716600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:66696800-66717600	Weak transcription	Fetal Brain Male	brain
5	chr12:66696800-66719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:66696800-66723600	Weak transcription	HSMM	muscle
7	chr12:66696800-66734200	Weak transcription	HSMMtube	muscle
8	chr12:66697000-66704400	Weak transcription	Brain Germinal Matrix	brain
9	chr12:66697000-66725000	Weak transcription	Ovary	ovary
10	chr12:66697200-66703600	Weak transcription	Spleen	Spleen
11	chr12:66697200-66703800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:66697200-66704000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:66697200-66707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:66697200-66716000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:66697200-66725600	Weak transcription	Fetal Heart	heart
16	chr12:66697200-66733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:66697200-66734800	Weak transcription	Esophagus	oesophagus
18	chr12:66697200-66735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:66697400-66703800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:66697400-66703800	Weak transcription	Gastric	stomach
22	chr12:66697400-66704000	Weak transcription	Fetal Intestine Small	intestine
23	chr12:66697400-66707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:66697400-66714800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:66697400-66719800	Weak transcription	Psoas Muscle	Psoas
26	chr12:66697400-66724800	Weak transcription	Pancreas	Pancrea
27	chr12:66697400-66732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:66697400-66732400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:66697400-66735000	Weak transcription	Right Ventricle	heart
30	chr12:66697600-66703600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:66697600-66714600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:66697800-66702200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:66697800-66703200	Weak transcription	Liver	Liver
34	chr12:66697800-66703400	Weak transcription	Adipose Nuclei	Adipose
35	chr12:66697800-66703400	Weak transcription	Placenta	Placenta
36	chr12:66697800-66703600	Weak transcription	Fetal Intestine Large	intestine
37	chr12:66697800-66703800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:66697800-66704000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:66697800-66704200	Weak transcription	Fetal Stomach	stomach
40	chr12:66697800-66725000	Weak transcription	Colonic Mucosa	Colon
41	chr12:66698000-66703600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:66698200-66703400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:66698200-66705800	Weak transcription	Stomach Mucosa	stomach
44	chr12:66698200-66707400	Weak transcription	Small Intestine	intestine
45	chr12:66698200-66707600	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:66698200-66725200	Weak transcription	Colon Smooth Muscle	Colon
47	chr12:66698200-66735000	Weak transcription	Fetal Brain Female	brain
48	chr12:66698400-66702200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:66698400-66702400	Weak transcription	Fetal Lung	lung
50	chr12:66698400-66702400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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