Variant report

Variant	rs2305008
Chromosome Location	chr11:120319064-120319065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:120318993-120319281	HepG2	liver:	n/a	chr11:120319138-120319158 chr11:120319148-120319159 chr11:120319146-120319160 chr11:120319143-120319159 chr11:120319148-120319159 chr11:120319143-120319158
2	MAFK	chr11:120319008-120319295	IMR90	lung:	n/a	chr11:120319138-120319158 chr11:120319148-120319159 chr11:120319146-120319160 chr11:120319143-120319159 chr11:120319148-120319159 chr11:120319143-120319158
3	MAFF	chr11:120318973-120319287	K562	blood:	n/a	chr11:120319141-120319155 chr11:120319142-120319160
4	MAFK	chr11:120319046-120319246	K562	blood:	n/a	chr11:120319138-120319158 chr11:120319148-120319159 chr11:120319146-120319160 chr11:120319143-120319159 chr11:120319148-120319159 chr11:120319143-120319158
5	MAFF	chr11:120318991-120319308	HepG2	liver:	n/a	chr11:120319141-120319155 chr11:120319142-120319160
6	MAFK	chr11:120318980-120319312	HepG2	liver:	n/a	chr11:120319138-120319158 chr11:120319148-120319159 chr11:120319146-120319160 chr11:120319143-120319159 chr11:120319148-120319159 chr11:120319143-120319158

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120311224..120316272-chr11:120317740..120322611,5	K562	blood:

Variant related genes	Relation type
ARHGEF12	TF binding region
ENSG00000196914	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10502235	0.90[JPT][hapmap]
rs10750172	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10750173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10750174	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10790378	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10790380	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10790382	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10790383	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10892562	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10892563	0.92[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10892564	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10892566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892567	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10892570	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10892574	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10892576	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10892578	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892582	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217821	0.81[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs11217840	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217841	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217852	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11217874	0.84[JPT][hapmap]
rs11217875	0.89[JPT][hapmap]
rs11217887	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11600703	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11601535	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11827818	0.84[JPT][hapmap]
rs12417256	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12420378	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12787285	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12794946	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12806740	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs1373270	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1892894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1893261	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2276035	0.84[JPT][hapmap]
rs2305010	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809059	0.81[JPT][hapmap]
rs4381380	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4539328	0.80[EUR][1000 genomes]
rs4936517	0.86[EUR][1000 genomes]
rs4938799	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs4938801	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4938804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4938805	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4938806	0.92[EUR][1000 genomes]
rs4938807	0.90[JPT][hapmap]
rs4938808	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs496248	0.81[JPT][hapmap]
rs632137	0.81[JPT][hapmap]
rs6589810	0.87[EUR][1000 genomes]
rs6589811	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6589812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6589813	0.94[EUR][1000 genomes]
rs7101415	0.87[EUR][1000 genomes]
rs7104639	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7107211	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7115714	0.93[EUR][1000 genomes]
rs7117063	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117321	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118391	1.00[ASW][hapmap];0.95[GIH][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7121779	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7126328	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7129944	0.90[JPT][hapmap]
rs7131046	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7131597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs723937	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7478880	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7924772	0.86[EUR][1000 genomes]
rs7924963	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924975	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7932037	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7933086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7937612	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7939137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7948928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7951250	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894839	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]
rs9633919	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9633950	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2305008	ARHGEF12	cis	cerebellum	SCAN
rs2305008	TMEM136	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120272400-120320600	Weak transcription	Psoas Muscle	Psoas
2	chr11:120275600-120322200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:120277600-120319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:120285600-120319800	Weak transcription	Gastric	stomach
5	chr11:120291800-120319200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:120301400-120355200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:120303000-120319400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:120303600-120355600	Weak transcription	Stomach Mucosa	stomach
9	chr11:120303800-120328000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:120304400-120323200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:120304600-120329800	Strong transcription	HSMM	muscle
12	chr11:120304800-120359400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:120306600-120341200	Strong transcription	Osteobl	bone
14	chr11:120306800-120319800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:120306800-120341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:120307000-120335800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr11:120307000-120341200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:120307600-120334600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:120308000-120319200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:120308000-120341800	Strong transcription	Fetal Intestine Large	intestine
21	chr11:120308000-120352600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:120308000-120359000	Strong transcription	Placenta	Placenta
23	chr11:120308200-120330600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:120308200-120336400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr11:120308400-120333200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:120308400-120334600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr11:120308400-120339000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:120308400-120339000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr11:120308400-120357800	Strong transcription	Adipose Nuclei	Adipose
30	chr11:120309600-120320000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr11:120309800-120333800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:120310000-120336000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:120310200-120350600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:120310400-120358000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:120310800-120333800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:120311200-120357200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:120312000-120328800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr11:120312000-120333800	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr11:120312200-120323600	Strong transcription	Fetal Lung	lung
40	chr11:120312200-120333000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:120312200-120339000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:120312400-120319800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:120312400-120326800	Strong transcription	HSMMtube	muscle
44	chr11:120312400-120328400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:120312400-120329800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr11:120312400-120341800	Strong transcription	Fetal Muscle Leg	muscle
47	chr11:120312400-120351800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr11:120312400-120354000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:120312800-120334000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr11:120312800-120357800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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