Variant report

Variant	rs7940880
Chromosome Location	chr11:74317414-74317415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74303636..74305531-chr11:74316171..74317855,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077514	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10219203	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793092	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10793093	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10793094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793098	0.87[ASN][1000 genomes]
rs10899009	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10899020	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899024	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11236158	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11236161	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236164	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236178	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236182	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11236188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11236189	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11604752	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12282266	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12421429	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1944933	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2117222	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2155935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298792	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3824999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4644667	0.89[ASN][1000 genomes]
rs57796856	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58659624	0.90[ASN][1000 genomes]
rs59830047	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60085010	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7103197	0.91[ASN][1000 genomes]
rs7121958	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7124188	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72977282	0.96[ASN][1000 genomes]
rs7924706	0.96[ASN][1000 genomes]
rs7932922	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7937753	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription 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 miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv832209	chr11:74155883-74329119	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv897914	chr11:74266026-74327614	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv897915	chr11:74269817-74327614	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7940880	ARHGEF17	cis	parietal	SCAN
rs7940880	RNF121	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74304400-74345600	Weak transcription	Gastric	stomach
2	chr11:74304600-74323600	Weak transcription	Brain Substantia Nigra	brain
3	chr11:74304600-74323600	Weak transcription	HSMMtube	muscle
4	chr11:74304600-74323800	Weak transcription	Brain Angular Gyrus	brain
5	chr11:74304600-74331400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:74304600-74345600	Weak transcription	Esophagus	oesophagus
7	chr11:74304600-74373800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:74304800-74323600	Weak transcription	Stomach Mucosa	stomach
9	chr11:74304800-74324000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr11:74304800-74336200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:74304800-74357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:74304800-74361400	Weak transcription	Colonic Mucosa	Colon
13	chr11:74305000-74322200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:74305000-74323000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:74305200-74318200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:74305200-74323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:74305200-74323600	Weak transcription	HUVEC	blood vessel
18	chr11:74305200-74331800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:74305400-74318400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr11:74305400-74319800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:74305400-74322600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr11:74305600-74320800	Weak transcription	HepG2	liver
23	chr11:74305600-74321400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:74305600-74324800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:74306400-74317800	Strong transcription	Dnd41	blood
26	chr11:74306600-74317600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:74307000-74319200	Strong transcription	Fetal Thymus	thymus
28	chr11:74307600-74317800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr11:74308400-74319600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:74308800-74319600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:74308800-74321800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:74308800-74329000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr11:74309600-74317800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:74309600-74322200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:74309600-74324600	Weak transcription	Right Ventricle	heart
36	chr11:74310000-74320800	Weak transcription	Fetal Brain Female	brain
37	chr11:74310000-74323400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:74310000-74323800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:74310200-74322400	Weak transcription	NH-A	brain
40	chr11:74310200-74352400	Weak transcription	Fetal Brain Male	brain
41	chr11:74310400-74323600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:74310400-74323600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:74310800-74318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:74311600-74337200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr11:74311800-74340600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr11:74312600-74317800	Strong transcription	Primary T cells from cord blood	blood
47	chr11:74312800-74318200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr11:74313000-74319800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:74313400-74318000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:74313600-74323800	Weak transcription	Brain Germinal Matrix	brain

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