Variant report

Variant	rs7135142
Chromosome Location	chr12:57672913-57672914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57672890..57675750-chr12:57846297..57849294,2	K562	blood:
2	chr12:57671194..57673496-chr12:57680187..57682848,2	K562	blood:
3	chr12:57672368..57674775-chr12:57822497..57825097,2	K562	blood:
4	chr12:57671280..57675750-chr12:57846169..57850162,4	K562	blood:

Variant related genes	Relation type
ENSG00000139269	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000258001	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10747777	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747778	1.00[CEU][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783818	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783819	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783820	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783823	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10876976	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes]
rs10876978	0.80[AMR][1000 genomes]
rs11172156	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172160	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172165	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11172169	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172170	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11172177	0.81[ASN][1000 genomes]
rs11172190	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11609986	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12296766	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12310220	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12579911	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12812140	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1798710	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs2063778	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2280139	0.95[JPT][hapmap]
rs35032945	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923885	0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4075325	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4760192	0.89[EUR][1000 genomes]
rs4760193	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4760228	0.82[AMR][1000 genomes]
rs4760236	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs4760308	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760348	0.96[CEU][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4760356	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4760357	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs481196	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs491750	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs512223	0.82[AMR][1000 genomes]
rs533975	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs537482	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs543410	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs560048	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs568793	0.80[JPT][hapmap]
rs575153	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs6581131	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6581134	0.85[CHB][hapmap];0.98[GIH][hapmap];0.84[LWK][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6581135	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6581136	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6581139	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7132367	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs7133366	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7133939	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7298418	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7307059	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7309659	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7313824	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7314266	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7358684	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7398058	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7486863	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7977908	0.96[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7135142	OR6C4	cis	parietal	SCAN
rs7135142	TSPAN31	cis	cerebellum	SCAN
rs7135142	DKFZP586D0919	cis	multi-tissue	Pritchard
rs7135142	SILV	cis	parietal	SCAN
rs7135142	XRCC6BP1	cis	multi-tissue	Pritchard
rs7135142	SPRY2	trans	lymphoblastoid	seeQTL
rs7135142	ZNF385A	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57638800-57673600	Weak transcription	Stomach Mucosa	stomach
2	chr12:57652000-57673600	Weak transcription	Hela-S3	cervix
3	chr12:57654800-57705400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57655800-57674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:57656200-57673800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:57656600-57682800	Weak transcription	Fetal Brain Male	brain
7	chr12:57658200-57673600	Strong transcription	Fetal Thymus	thymus
8	chr12:57660600-57674200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:57662800-57674200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:57662800-57706000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr12:57663000-57674000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:57663800-57673400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:57663800-57673400	Weak transcription	Brain Substantia Nigra	brain
14	chr12:57663800-57673600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:57663800-57675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:57664000-57673400	Weak transcription	NH-A	brain
17	chr12:57664000-57674000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:57665200-57673400	Weak transcription	NHEK	skin
19	chr12:57665400-57674000	Weak transcription	Pancreas	Pancrea
20	chr12:57665600-57673400	Weak transcription	Fetal Lung	lung
21	chr12:57667000-57674000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:57667000-57674000	Weak transcription	Right Ventricle	heart
23	chr12:57667200-57673400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:57667600-57673800	Weak transcription	HUVEC	blood vessel
25	chr12:57667600-57674000	Weak transcription	Aorta	Aorta
26	chr12:57667600-57674000	Weak transcription	Esophagus	oesophagus
27	chr12:57667600-57675600	Weak transcription	Gastric	stomach
28	chr12:57667600-57685600	Weak transcription	Fetal Heart	heart
29	chr12:57667600-57687200	Weak transcription	Psoas Muscle	Psoas
30	chr12:57667800-57673800	Weak transcription	HSMMtube	muscle
31	chr12:57668000-57673600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:57668400-57673600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:57669000-57674000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr12:57669400-57674000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:57669400-57674200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:57669600-57673400	Strong transcription	Fetal Intestine Small	intestine
37	chr12:57669600-57678600	Strong transcription	Fetal Stomach	stomach
38	chr12:57670000-57673600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:57670000-57674000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:57670200-57673400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:57670200-57681400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr12:57670400-57674000	Strong transcription	Placenta	Placenta
43	chr12:57670400-57707000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:57670600-57673200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:57670600-57673400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:57670600-57673400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:57670600-57673600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:57670600-57673600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:57670600-57673600	Strong transcription	Dnd41	blood
50	chr12:57670600-57673800	Strong transcription	Duodenum Mucosa	Duodenum

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