Variant report

Variant	rs894839
Chromosome Location	chr11:120337705-120337706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120327757..120329362-chr11:120335965..120337981,2	K562	blood:
2	chr11:120335178..120336846-chr11:120337468..120340441,2	MCF-7	breast:
3	chr11:120337304..120339798-chr11:120344067..120345617,2	K562	blood:

Variant related genes	Relation type
ENSG00000196914	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10502235	0.90[JPT][hapmap]
rs10750172	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10750173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10750174	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10790378	0.83[EUR][1000 genomes]
rs10790380	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10790382	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10790383	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892562	0.84[EUR][1000 genomes]
rs10892563	0.82[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10892564	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10892566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10892567	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10892570	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10892574	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10892576	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10892578	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10892582	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217821	0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap]
rs11217840	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11217841	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11217852	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11217874	0.84[JPT][hapmap]
rs11217875	0.89[JPT][hapmap]
rs11217887	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11600703	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11601535	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827818	0.84[JPT][hapmap]
rs12417256	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420378	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12787285	0.86[EUR][1000 genomes]
rs12794946	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12806740	0.82[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs1373270	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1892894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1893261	0.88[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs2276035	0.84[JPT][hapmap]
rs2305008	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305010	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809059	0.81[JPT][hapmap]
rs4381380	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs4539328	0.80[EUR][1000 genomes]
rs4936517	0.85[EUR][1000 genomes]
rs4938799	0.88[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs4938801	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4938804	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4938805	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4938806	0.91[EUR][1000 genomes]
rs4938807	0.90[JPT][hapmap]
rs4938808	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496248	0.81[JPT][hapmap]
rs632137	0.81[JPT][hapmap]
rs6589810	0.86[EUR][1000 genomes]
rs6589811	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6589812	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6589813	0.93[EUR][1000 genomes]
rs7101415	0.86[EUR][1000 genomes]
rs7104639	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7107211	0.90[EUR][1000 genomes]
rs7115714	0.92[EUR][1000 genomes]
rs7117063	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7117321	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7118391	0.81[ASW][hapmap];0.98[GIH][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7121779	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7126328	0.86[EUR][1000 genomes]
rs7129944	0.90[JPT][hapmap]
rs7131046	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7131597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723937	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7478880	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924772	0.85[EUR][1000 genomes]
rs7924963	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7924975	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7932037	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7933086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7937612	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7939137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7951250	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9633919	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9633950	0.87[EUR][1000 genomes];0.90[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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv529003	chr11:120209386-120355230	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs894839	ARHGEF12	cis	cerebellum	SCAN
rs894839	TMEM136	cis	parietal	SCAN
rs894839	TMEM136	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120301400-120355200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:120303600-120355600	Weak transcription	Stomach Mucosa	stomach
3	chr11:120304800-120359400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:120306600-120341200	Strong transcription	Osteobl	bone
5	chr11:120306800-120341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:120307000-120341200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:120308000-120341800	Strong transcription	Fetal Intestine Large	intestine
8	chr11:120308000-120352600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:120308000-120359000	Strong transcription	Placenta	Placenta
10	chr11:120308400-120339000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:120308400-120339000	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr11:120308400-120357800	Strong transcription	Adipose Nuclei	Adipose
13	chr11:120310200-120350600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:120310400-120358000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:120311200-120357200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:120312200-120339000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:120312400-120341800	Strong transcription	Fetal Muscle Leg	muscle
18	chr11:120312400-120351800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:120312400-120354000	Strong transcription	Duodenum Mucosa	Duodenum
20	chr11:120312800-120357800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:120314200-120362200	Strong transcription	Liver	Liver
22	chr11:120314800-120342000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:120315200-120353000	Strong transcription	Fetal Brain Female	brain
24	chr11:120315400-120342400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr11:120316400-120382000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:120317400-120343200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:120319200-120339200	Strong transcription	Fetal Kidney	kidney
28	chr11:120319200-120341400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:120319800-120342400	Strong transcription	HUVEC	blood vessel
30	chr11:120320000-120350600	Weak transcription	Hela-S3	cervix
31	chr11:120320000-120358000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:120320200-120357600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:120321000-120338800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr11:120321000-120358000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:120321200-120350800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:120323600-120348800	Weak transcription	Spleen	Spleen
37	chr11:120325600-120350600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:120327200-120338800	Strong transcription	Left Ventricle	heart
39	chr11:120327400-120342000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:120328400-120345600	Weak transcription	Pancreas	Pancrea
41	chr11:120328400-120347800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:120329000-120358800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:120329200-120338800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:120329600-120342000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:120329600-120345600	Weak transcription	Primary B cells from cord blood	blood
46	chr11:120330600-120341000	Strong transcription	HSMM	muscle
47	chr11:120330600-120342600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:120331000-120341400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:120331200-120340800	Strong transcription	NHDF-Ad	bronchial
50	chr11:120331600-120339000	Strong transcription	Ovary	ovary

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