Variant report

Variant	rs6764415
Chromosome Location	chr3:48512195-48512196
allele	A/G
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	POLR2A	chr3:48507011-48512604	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:48509593-48512943	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48510260..48512404-chr3:48592890..48595693,2	MCF-7	breast:
2	chr3:48511787..48515469-chr3:48539737..48543035,4	K562	blood:
3	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:

Variant related genes	Relation type
SHISA5	TF binding region
ENSG00000114268	Chromatin interaction
ENSG00000164054	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1037773	0.84[EUR][1000 genomes]
rs10470686	0.83[EUR][1000 genomes]
rs1109227	0.84[EUR][1000 genomes]
rs11130170	0.83[EUR][1000 genomes]
rs11130171	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11712561	0.82[EUR][1000 genomes]
rs11797	0.85[EUR][1000 genomes]
rs12487542	0.82[EUR][1000 genomes]
rs13069724	0.84[EUR][1000 genomes]
rs13071337	0.82[EUR][1000 genomes]
rs13072012	0.86[EUR][1000 genomes]
rs13076076	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13091785	0.88[EUR][1000 genomes]
rs13314659	0.83[EUR][1000 genomes]
rs13324374	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1459249	0.84[EUR][1000 genomes]
rs1459250	0.81[AMR][1000 genomes]
rs1563736	0.82[EUR][1000 genomes]
rs1870444	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1975844	0.82[EUR][1000 genomes]
rs2045554	0.87[EUR][1000 genomes]
rs2242150	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2279077	0.84[EUR][1000 genomes]
rs2290822	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2362450	0.84[EUR][1000 genomes]
rs28824259	0.82[EUR][1000 genomes]
rs3214041	0.83[EUR][1000 genomes]
rs34761139	0.82[EUR][1000 genomes]
rs35215722	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3774808	0.84[EUR][1000 genomes]
rs4490383	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4858795	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56298324	0.81[EUR][1000 genomes]
rs60512868	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6442118	0.83[EUR][1000 genomes]
rs6442119	0.83[EUR][1000 genomes]
rs6442120	0.85[EUR][1000 genomes]
rs6442123	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6442124	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6770470	0.83[EUR][1000 genomes]
rs6776700	0.89[EUR][1000 genomes]
rs6784322	0.80[EUR][1000 genomes]
rs6784541	0.80[EUR][1000 genomes]
rs6794875	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6796491	0.82[EUR][1000 genomes]
rs6800475	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6804774	0.82[EUR][1000 genomes]
rs6810060	0.81[EUR][1000 genomes]
rs7126	0.86[EUR][1000 genomes]
rs73074358	0.82[EUR][1000 genomes]
rs734071	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs734072	0.89[ASN][1000 genomes]
rs7618883	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7634377	0.80[EUR][1000 genomes]
rs7635522	0.82[EUR][1000 genomes]
rs7636044	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7639743	0.83[AMR][1000 genomes]
rs922075	0.86[EUR][1000 genomes]
rs9311423	0.80[EUR][1000 genomes]
rs9311424	0.80[EUR][1000 genomes]
rs9311428	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9809843	0.82[EUR][1000 genomes]
rs9812647	0.83[EUR][1000 genomes]
rs9815088	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9826195	0.82[EUR][1000 genomes]
rs9826247	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9838618	0.86[EUR][1000 genomes]
rs9849509	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9862575	0.82[EUR][1000 genomes]
rs9864371	0.82[EUR][1000 genomes]
rs9864815	0.82[EUR][1000 genomes]
rs9875280	0.82[EUR][1000 genomes]
rs9876781	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9876891	0.84[EUR][1000 genomes]
rs9881491	0.85[EUR][1000 genomes]
rs9883759	0.85[EUR][1000 genomes]
rs9883927	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6764415	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs6764415	TMA7	cis	Muscle Skeletal	GTEx
rs6764415	RP11-24C3.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48506400-48512600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:48506600-48513600	Enhancers	Fetal Brain Male	brain
3	chr3:48508200-48512600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:48508400-48512200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:48508400-48513400	Genic enhancers	Fetal Intestine Small	intestine
6	chr3:48508400-48513800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:48508600-48512200	Genic enhancers	Gastric	stomach
8	chr3:48508600-48512800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:48508600-48513400	Weak transcription	K562	blood
10	chr3:48508800-48512200	Genic enhancers	Lung	lung
11	chr3:48508800-48512200	Genic enhancers	Spleen	Spleen
12	chr3:48508800-48512600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:48508800-48512600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:48508800-48512600	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr3:48508800-48513600	Weak transcription	Fetal Kidney	kidney
16	chr3:48508800-48513800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:48509000-48512200	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:48509000-48512200	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr3:48509000-48512200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:48509000-48512400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:48509000-48512600	Genic enhancers	Fetal Muscle Leg	muscle
22	chr3:48509000-48512600	Enhancers	Stomach Mucosa	stomach
23	chr3:48509000-48512800	Genic enhancers	Brain Cingulate Gyrus	brain
24	chr3:48509000-48514200	Weak transcription	Fetal Heart	heart
25	chr3:48509200-48512600	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr3:48509200-48513400	Weak transcription	NH-A	brain
27	chr3:48509400-48512200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:48509400-48512200	Genic enhancers	Colonic Mucosa	Colon
29	chr3:48509600-48512600	Weak transcription	HUVEC	blood vessel
30	chr3:48509600-48513400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:48509600-48513800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:48509800-48512200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:48509800-48512200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:48509800-48512200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:48510000-48512200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:48510000-48513400	Weak transcription	HMEC	breast
37	chr3:48510200-48512200	Genic enhancers	Duodenum Mucosa	Duodenum
38	chr3:48510200-48512400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:48510200-48512600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:48510200-48513400	Weak transcription	NHDF-Ad	bronchial
41	chr3:48510800-48512800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:48510800-48513600	Enhancers	Small Intestine	intestine
43	chr3:48511000-48512400	Enhancers	HepG2	liver
44	chr3:48511000-48513400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr3:48511000-48513400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:48511000-48513600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:48511000-48513800	Weak transcription	Aorta	Aorta
48	chr3:48511000-48514000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:48511200-48512600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:48511200-48512600	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links