Variant report

Variant	rs7930507
Chromosome Location	chr11:9192702-9192703
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	chr11:9190584..9193307-chr11:9197709..9200667,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184014	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10047438	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1039210	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769991	0.86[CHB][hapmap]
rs10769992	0.84[CEU][hapmap]
rs10769994	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10769995	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10769996	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10769997	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10769998	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10769999	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10840175	0.82[EUR][1000 genomes]
rs10840176	0.81[EUR][1000 genomes]
rs10840183	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10840185	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10840202	0.82[CHD][hapmap]
rs11042189	0.81[EUR][1000 genomes]
rs11042199	0.86[CHB][hapmap]
rs11042200	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042211	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11042213	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12099067	0.86[CHD][hapmap]
rs12286943	0.82[CHD][hapmap]
rs12291375	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17256375	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs1827011	0.80[CEU][hapmap];0.91[MEX][hapmap]
rs1874822	0.87[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs2133217	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2291839	0.91[CHD][hapmap]
rs2316087	0.81[EUR][1000 genomes]
rs2647533	0.83[MEX][hapmap]
rs2647537	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs2742556	0.84[CEU][hapmap];0.91[MEX][hapmap]
rs4537761	0.82[CHD][hapmap]
rs6486199	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6486206	0.89[YRI][hapmap]
rs6486210	0.95[YRI][hapmap]
rs6486231	0.94[YRI][hapmap]
rs7109745	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7112540	0.95[YRI][hapmap]
rs7114688	0.95[YRI][hapmap]
rs7120239	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7123970	0.88[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.83[ASN][1000 genomes]
rs7394878	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7395151	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7395347	0.86[CHB][hapmap]
rs7395846	0.91[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs7396439	0.95[YRI][hapmap]
rs7396705	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7925308	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7925418	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7931872	0.81[EUR][1000 genomes]
rs7947251	0.84[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs956517	0.84[ASN][1000 genomes]
rs9888257	0.86[CHB][hapmap];0.91[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7930507	OR56A1	cis	cerebellum	SCAN
rs7930507	EIF4G2	cis	cerebellum	SCAN
rs7930507	TRIM5	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9155000-9203400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:9161200-9202400	Weak transcription	Small Intestine	intestine
3	chr11:9162000-9230600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:9166000-9200600	Weak transcription	Colonic Mucosa	Colon
5	chr11:9169200-9198400	Weak transcription	Thymus	Thymus
6	chr11:9169600-9238000	Weak transcription	Esophagus	oesophagus
7	chr11:9171800-9230200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:9172000-9230400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:9172200-9197800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:9172200-9199600	Weak transcription	Gastric	stomach
11	chr11:9173000-9199400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:9173400-9199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:9173600-9199600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:9174000-9194800	Weak transcription	Fetal Kidney	kidney
15	chr11:9174000-9198200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:9174000-9199400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:9174000-9225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:9175800-9193000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:9178200-9195400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:9180000-9199600	Weak transcription	Aorta	Aorta
21	chr11:9182400-9225000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr11:9182400-9231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:9182600-9198000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:9182600-9199000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:9182600-9199600	Weak transcription	Fetal Brain Male	brain
26	chr11:9183000-9195400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:9184000-9193000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:9184000-9195200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:9184000-9195400	Strong transcription	Fetal Stomach	stomach
30	chr11:9184000-9195600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:9184200-9208200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:9184200-9216800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:9186000-9195400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr11:9186000-9195400	Strong transcription	Adipose Nuclei	Adipose
35	chr11:9186800-9195400	Strong transcription	Fetal Muscle Leg	muscle
36	chr11:9186800-9215800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:9187000-9195400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:9187200-9195000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:9187200-9195200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr11:9187200-9197800	Weak transcription	Brain Germinal Matrix	brain
41	chr11:9187600-9201800	Weak transcription	Pancreas	Pancrea
42	chr11:9188800-9195000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:9189000-9195200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr11:9189200-9195200	Strong transcription	Placenta	Placenta
45	chr11:9189400-9192800	Strong transcription	Fetal Thymus	thymus
46	chr11:9189400-9193000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:9189400-9194200	Strong transcription	Primary T cells from cord blood	blood
48	chr11:9189400-9195200	Strong transcription	Primary B cells from cord blood	blood
49	chr11:9189800-9194200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:9190000-9193000	Strong transcription	Primary B cells from peripheral blood	blood

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