Variant report

Variant	rs11130237
Chromosome Location	chr3:50039303-50039304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs11130223	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130225	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130239	0.86[GIH][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130240	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11919418	1.00[JPT][hapmap]
rs11920034	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11923132	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11924711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11925156	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11928995	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12486470	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12486808	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486832	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492291	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12493565	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494077	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494172	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494916	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12495114	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12495831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629677	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630917	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12630959	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12631306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631309	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631608	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632751	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12636045	0.83[AMR][1000 genomes]
rs12636232	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs12636669	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637222	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637457	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637681	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12638046	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12639175	1.00[JPT][hapmap]
rs1317215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs13326300	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2023951	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2023952	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2188151	1.00[JPT][hapmap]
rs2518796	1.00[JPT][hapmap]
rs28478136	0.92[EUR][1000 genomes]
rs35333166	0.83[AMR][1000 genomes]
rs41291716	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55643042	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57009357	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57575459	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58025924	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58621288	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58766761	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59802870	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61263937	0.89[EUR][1000 genomes]
rs61491513	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61729114	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62260717	0.80[EUR][1000 genomes]
rs62260756	0.92[EUR][1000 genomes]
rs62260770	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs62260771	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs62262060	0.92[EUR][1000 genomes]
rs62262095	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262096	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262099	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262100	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262104	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262105	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262116	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262117	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262136	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262138	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262144	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262145	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262148	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263578	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263580	0.88[EUR][1000 genomes]
rs62263584	0.88[EUR][1000 genomes]
rs62263586	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263588	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263590	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62263591	0.84[EUR][1000 genomes]
rs62263596	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs62263597	0.89[AMR][1000 genomes]
rs62263600	0.83[AMR][1000 genomes]
rs6797500	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs9813644	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9859813	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11130237	MON1A	cis	multi-tissue	Pritchard
rs11130237	BSN	cis	multi-tissue	Pritchard
rs11130237	BSN	cis	Liver	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:49998400-50078600	Weak transcription	K562	blood
4	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
7	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
9	chr3:50006200-50040800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:50010800-50087000	Weak transcription	NHLF	lung
12	chr3:50011000-50041000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:50011000-50046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:50011000-50046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:50011000-50048400	Weak transcription	A549	lung
16	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
17	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
19	chr3:50012400-50049000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:50015400-50046400	Weak transcription	Fetal Kidney	kidney
22	chr3:50015800-50041000	Weak transcription	HSMMtube	muscle
23	chr3:50016000-50040800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:50018800-50043600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:50022200-50046400	Weak transcription	Gastric	stomach
26	chr3:50022600-50041200	Weak transcription	Aorta	Aorta
27	chr3:50027600-50040000	Strong transcription	Primary T cells from cord blood	blood
28	chr3:50028000-50056400	Weak transcription	Ovary	ovary
29	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
30	chr3:50029200-50041000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:50029800-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
33	chr3:50031000-50048000	Strong transcription	Fetal Thymus	thymus
34	chr3:50031200-50039800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:50031400-50039800	Strong transcription	Dnd41	blood
36	chr3:50031600-50039600	Strong transcription	Liver	Liver
37	chr3:50031600-50039800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:50031800-50039600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:50031800-50039800	Strong transcription	Primary B cells from cord blood	blood
40	chr3:50032000-50040200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:50033400-50039600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:50033400-50039800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:50033400-50041400	Strong transcription	Fetal Lung	lung
44	chr3:50033800-50051000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:50034800-50039600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:50035000-50040000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
48	chr3:50035600-50039600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:50035600-50039600	Strong transcription	Left Ventricle	heart
50	chr3:50035600-50040200	Strong transcription	Primary neutrophils fromperipheralblood	blood

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