Variant report

Variant	rs9311428
Chromosome Location	chr3:48520289-48520290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48514357..48516464-chr3:48518099..48520580,2	K562	blood:
2	chr3:48513069..48515559-chr3:48519678..48521467,2	K562	blood:
3	chr3:48519627..48521356-chr3:48540019..48542840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164054	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1037773	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs10470686	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1109227	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs11130170	0.90[JPT][hapmap]
rs11130171	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs11797	0.84[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs12491849	0.81[GIH][hapmap]
rs13076076	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs13314659	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs1459242	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1563736	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs2242150	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs2279077	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs2290822	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs2362450	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2362452	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs2885510	0.94[JPT][hapmap]
rs3214041	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs3774808	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs4858795	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858819	0.85[JPT][hapmap]
rs6442117	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6442118	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6442119	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6442120	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs6764415	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6776700	0.84[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs6794875	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs725309	0.89[JPT][hapmap]
rs725310	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs730566	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs734071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs734072	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636044	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7651407	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs898225	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs922075	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs9812647	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs9815088	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815103	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs9838618	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9849509	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9876781	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9883759	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs9883927	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]

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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9311428	ATRIP	cis	Cerebellum	GTEx
rs9311428	TMA7	cis	Muscle Skeletal	GTEx
rs9311428	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs9311428	SHISA5	cis	lymphoblastoid	seeQTL
rs9311428	CXCR6	cis	parietal	SCAN
rs9311428	C3orf18	cis	cerebellum	SCAN
rs9311428	PLXNB1	cis	lymphoblastoid	seeQTL
rs9311428	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs9311428	PLXNB1	cis	multi-tissue	Pritchard
rs9311428	AMT	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48514600-48535600	Weak transcription	Ovary	ovary
2	chr3:48514800-48541000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:48515000-48520400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:48515000-48522600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:48515000-48532800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:48515000-48533000	Weak transcription	NH-A	brain
7	chr3:48515000-48535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:48515000-48535600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:48515000-48537400	Weak transcription	NHLF	lung
10	chr3:48515000-48539600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:48515000-48539800	Weak transcription	Osteobl	bone
12	chr3:48515000-48540200	Weak transcription	NHDF-Ad	bronchial
13	chr3:48515000-48540400	Weak transcription	HSMM	muscle
14	chr3:48515000-48541000	Weak transcription	Aorta	Aorta
15	chr3:48515200-48520400	Weak transcription	Colonic Mucosa	Colon
16	chr3:48515200-48520400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:48515200-48520600	Weak transcription	NHEK	skin
18	chr3:48515200-48522000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:48515200-48535000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:48515200-48535000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:48515200-48535600	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:48515200-48535600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:48515200-48537400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:48515200-48538600	Weak transcription	Small Intestine	intestine
25	chr3:48515200-48539800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:48515200-48540000	Weak transcription	Brain Angular Gyrus	brain
27	chr3:48515200-48540200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:48515200-48540200	Weak transcription	HUVEC	blood vessel
29	chr3:48515200-48540400	Weak transcription	Fetal Brain Female	brain
30	chr3:48515200-48540600	Weak transcription	Brain Germinal Matrix	brain
31	chr3:48515200-48540600	Weak transcription	Fetal Lung	lung
32	chr3:48515400-48520400	Weak transcription	Pancreas	Pancrea
33	chr3:48515400-48520400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:48515400-48535600	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:48515400-48538200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:48516200-48520800	Strong transcription	Fetal Stomach	stomach
37	chr3:48516200-48520800	Strong transcription	Gastric	stomach
38	chr3:48516200-48521000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:48516200-48521000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:48516400-48520400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:48516400-48520600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:48516600-48521000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:48516600-48535000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:48516600-48535600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:48516800-48520600	Strong transcription	Lung	lung
46	chr3:48516800-48520800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:48516800-48520800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:48516800-48521200	Strong transcription	Fetal Intestine Small	intestine
49	chr3:48516800-48534200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:48516800-48535600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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