Variant report

Variant	rs6488067
Chromosome Location	chr12:32742241-32742242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10047581	0.92[CHB][hapmap]
rs10129039	0.83[ASN][1000 genomes]
rs10129043	0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10161053	0.82[ASN][1000 genomes]
rs10743799	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10743800	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs10771964	0.91[EUR][1000 genomes]
rs10771965	0.99[ASN][1000 genomes]
rs10771966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10771967	1.00[ASN][1000 genomes]
rs10844249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10844250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10844251	0.92[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs11052090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11052094	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11052100	0.82[ASN][1000 genomes]
rs1472501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472502	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1909513	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs1979824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs1979826	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs2036267	0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2291882	0.99[ASN][1000 genomes]
rs2291883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2389102	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389103	1.00[ASN][1000 genomes]
rs2389104	1.00[ASN][1000 genomes]
rs4931018	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4931021	1.00[ASN][1000 genomes]
rs4931023	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931026	0.83[ASN][1000 genomes]
rs4931027	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4931639	0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4931640	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6488068	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488069	0.86[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6488070	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6488071	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7136686	0.92[EUR][1000 genomes]
rs7300661	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7308071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311621	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315971	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7316616	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7954226	0.92[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs7962088	1.00[ASN][1000 genomes]
rs7964734	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7965993	0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7968781	0.82[ASN][1000 genomes]
rs7968790	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7971634	0.98[ASN][1000 genomes]
rs7977053	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979016	0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs904582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9988998	0.88[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6488067	D4S234E	trans	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32713000-32780400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:32713400-32796200	Weak transcription	Fetal Lung	lung
3	chr12:32715200-32753800	Weak transcription	Fetal Brain Female	brain
4	chr12:32715200-32760200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:32720000-32764800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:32720200-32778400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:32721400-32743600	Weak transcription	Fetal Heart	heart
8	chr12:32722600-32754400	Weak transcription	Colonic Mucosa	Colon
9	chr12:32722600-32757600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:32722600-32764800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:32722600-32764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:32722600-32764800	Weak transcription	Psoas Muscle	Psoas
13	chr12:32722600-32779400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:32723600-32756600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:32725200-32743800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:32725200-32778600	Weak transcription	Fetal Brain Male	brain
17	chr12:32728600-32757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:32731800-32753400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:32732400-32744600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:32732400-32756600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:32733200-32764800	Weak transcription	Esophagus	oesophagus
22	chr12:32735400-32743600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:32735400-32758400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:32735400-32765000	Weak transcription	Small Intestine	intestine
25	chr12:32735600-32742600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:32735600-32744600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:32735600-32754400	Weak transcription	Aorta	Aorta
28	chr12:32735800-32753800	Weak transcription	Placenta	Placenta
29	chr12:32736200-32746400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr12:32736200-32764000	Weak transcription	Brain Germinal Matrix	brain
31	chr12:32736400-32744400	Weak transcription	Pancreas	Pancrea
32	chr12:32736400-32754200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:32736400-32760200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:32736600-32744200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:32736600-32747000	Weak transcription	Ovary	ovary
36	chr12:32736600-32757000	Weak transcription	HepG2	liver
37	chr12:32736800-32757400	Weak transcription	Fetal Kidney	kidney
38	chr12:32737200-32743400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:32737200-32754200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:32738200-32743200	Enhancers	Fetal Thymus	thymus
41	chr12:32738400-32743000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:32738400-32743800	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr12:32738600-32742800	Enhancers	Primary hematopoietic stem cells	blood
44	chr12:32738600-32742800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:32738600-32743200	Enhancers	Primary B cells from cord blood	blood
46	chr12:32738600-32743200	Enhancers	Dnd41	blood
47	chr12:32738600-32743800	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:32738800-32744400	Weak transcription	Fetal Stomach	stomach
49	chr12:32738800-32744800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:32739000-32743600	Weak transcription	H1 Cell Line	embryonic stem cell

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