Variant report

Variant	rs734071
Chromosome Location	chr3:48519821-48519822
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	CTCF	chr3:48519820-48519970	GM12872	blood:	n/a	n/a

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
SHISA5	TF binding region
ENSG00000164054	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

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];0.85[YRI][hapmap]
rs11797	0.84[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs12491849	0.81[GIH][hapmap]
rs13062576	0.95[YRI][hapmap]
rs13076076	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][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];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
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];0.85[YRI][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];0.85[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[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]
rs6442123	0.83[AMR][1000 genomes]
rs6442124	0.81[AMR][1000 genomes]
rs6764415	0.84[AMR][1000 genomes];0.89[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]
rs734072	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636044	0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
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]
rs9311428	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]
rs9812647	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs9815088	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];0.85[YRI][hapmap]
rs9876781	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs9883759	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs9883927	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv590243	chr3:48505831-48519821	Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv590244	chr3:48505924-48519821	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv590245	chr3:48506222-48519821	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs734071	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs734071	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs734071	AMT	cis	cerebellum	SCAN
rs734071	PLXNB1	cis	lymphoblastoid	seeQTL
rs734071	CXCR6	cis	parietal	SCAN
rs734071	ATRIP	cis	Cerebellum	GTEx
rs734071	SHISA5	cis	lymphoblastoid	seeQTL
rs734071	C3orf18	cis	cerebellum	SCAN
rs734071	TMA7	cis	Muscle Skeletal	GTEx

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	chr3:48515200-48520000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:48515200-48520400	Weak transcription	Colonic Mucosa	Colon
17	chr3:48515200-48520400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:48515200-48520600	Weak transcription	NHEK	skin
19	chr3:48515200-48522000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:48515200-48535000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:48515200-48535000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:48515200-48535600	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:48515200-48535600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:48515200-48537400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:48515200-48538600	Weak transcription	Small Intestine	intestine
26	chr3:48515200-48539800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:48515200-48540000	Weak transcription	Brain Angular Gyrus	brain
28	chr3:48515200-48540200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:48515200-48540200	Weak transcription	HUVEC	blood vessel
30	chr3:48515200-48540400	Weak transcription	Fetal Brain Female	brain
31	chr3:48515200-48540600	Weak transcription	Brain Germinal Matrix	brain
32	chr3:48515200-48540600	Weak transcription	Fetal Lung	lung
33	chr3:48515400-48520200	Weak transcription	HMEC	breast
34	chr3:48515400-48520400	Weak transcription	Pancreas	Pancrea
35	chr3:48515400-48520400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:48515400-48535600	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:48515400-48538200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:48516000-48520000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:48516200-48520800	Strong transcription	Fetal Stomach	stomach
40	chr3:48516200-48520800	Strong transcription	Gastric	stomach
41	chr3:48516200-48521000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:48516200-48521000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:48516400-48520400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:48516400-48520600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr3:48516600-48521000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:48516600-48535000	Weak transcription	Fetal Intestine Large	intestine
47	chr3:48516600-48535600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:48516800-48520600	Strong transcription	Lung	lung
49	chr3:48516800-48520800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:48516800-48520800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links