Variant report

Variant	rs9815088
Chromosome Location	chr3:48515947-48515948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr3:48515932-48516665	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr3:48515912-48516487	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr3:48515931-48516468	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF2	chr3:48515928-48516484	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP4	chr3:48515946-48516622	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48512815..48516100-chr3:48594601..48597600,3	K562	blood:
2	chr3:48514107..48516088-chr3:48667675..48669788,2	K562	blood:
3	chr3:48505885..48511674-chr3:48512501..48516993,10	K562	blood:
4	chr3:48481215..48483251-chr3:48514789..48517662,2	K562	blood:
5	chr3:48515040..48517957-chr3:48545083..48546816,2	MCF-7	breast:
6	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:
7	chr3:48515011..48517964-chr3:48519270..48521747,2	MCF-7	breast:
8	chr3:48514328..48516205-chr3:48592157..48594449,2	K562	blood:

No data

Variant related genes	Relation type
SHISA5	TF binding region
ENSG00000232112	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000225697	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11797	0.80[AMR][1000 genomes]
rs13091785	0.80[AMR][1000 genomes]
rs4858795	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6764415	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6776700	0.80[AMR][1000 genomes]
rs7126	0.80[AMR][1000 genomes]
rs734071	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs734072	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7618883	0.84[AMR][1000 genomes]
rs9311428	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826247	0.83[AMR][1000 genomes]
rs9838618	0.80[AMR][1000 genomes]
rs9881491	0.80[AMR][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
rs9815088	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs9815088	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs9815088	TMA7	cis	Muscle Skeletal	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48514600-48516800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:48514600-48535600	Weak transcription	Ovary	ovary
3	chr3:48514800-48516400	Enhancers	Placenta	Placenta
4	chr3:48514800-48541000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:48515000-48516200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:48515000-48516200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:48515000-48516200	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:48515000-48516200	Weak transcription	Esophagus	oesophagus
9	chr3:48515000-48516200	Weak transcription	Spleen	Spleen
10	chr3:48515000-48516400	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:48515000-48516600	Enhancers	Fetal Intestine Large	intestine
12	chr3:48515000-48516600	Enhancers	Fetal Intestine Small	intestine
13	chr3:48515000-48516800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:48515000-48519000	Weak transcription	Right Atrium	heart
15	chr3:48515000-48519000	Weak transcription	Right Ventricle	heart
16	chr3:48515000-48520400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:48515000-48522600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:48515000-48532800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:48515000-48533000	Weak transcription	NH-A	brain
20	chr3:48515000-48535600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:48515000-48535600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:48515000-48537400	Weak transcription	NHLF	lung
23	chr3:48515000-48539600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:48515000-48539800	Weak transcription	Osteobl	bone
25	chr3:48515000-48540200	Weak transcription	NHDF-Ad	bronchial
26	chr3:48515000-48540400	Weak transcription	HSMM	muscle
27	chr3:48515000-48541000	Weak transcription	Aorta	Aorta
28	chr3:48515200-48516200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:48515200-48516200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:48515200-48516200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:48515200-48516200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:48515200-48516200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:48515200-48516200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:48515200-48516200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:48515200-48516200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:48515200-48516200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:48515200-48516200	Weak transcription	Fetal Stomach	stomach
38	chr3:48515200-48516200	Weak transcription	Gastric	stomach
39	chr3:48515200-48516200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:48515200-48516400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:48515200-48516400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:48515200-48516400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:48515200-48516400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:48515200-48516600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:48515200-48516600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:48515200-48516600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:48515200-48516800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:48515200-48516800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:48515200-48516800	Weak transcription	Lung	lung
50	chr3:48515200-48517200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links