Variant report

Variant	rs13238478
Chromosome Location	chr7:66388082-66388083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:66385651..66388919-chr7:66460114..66462403,3	MCF-7	breast:
2	chr7:66386885..66388455-chr7:66393635..66395755,2	MCF-7	breast:
3	chr7:66204784..66206359-chr7:66385620..66388278,2	MCF-7	breast:
4	chr7:66384595..66388317-chr7:66459135..66463010,5	K562	blood:
5	chr7:66361028..66363688-chr7:66387186..66389228,2	K562	blood:
6	chr7:66379191..66382749-chr7:66384574..66388642,5	K562	blood:
7	chr7:66385188..66388317-chr7:66459133..66463010,3	K562	blood:
8	chr7:66384799..66388848-chr7:66389441..66396879,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000126524	Chromatin interaction
ENSG00000179131	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000106609	Chromatin interaction
ENSG00000198874	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000272831	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11763269	0.83[LWK][hapmap]
rs12698542	0.90[AFR][1000 genomes]
rs12698551	1.00[ASN][1000 genomes]
rs13228779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13229468	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13232393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13235282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13236129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13237544	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13238612	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13246227	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1573944	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1880644	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1922723	0.90[AFR][1000 genomes]
rs2141924	0.90[AFR][1000 genomes]
rs2178742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2659903	0.90[AFR][1000 genomes]
rs2707823	0.90[AFR][1000 genomes]
rs2707826	0.82[AFR][1000 genomes]
rs2707828	0.80[AFR][1000 genomes]
rs2707830	0.90[AFR][1000 genomes]
rs34162778	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34314366	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34423980	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34559676	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34785430	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34816289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35043782	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35111158	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];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35315599	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35390465	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35481333	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35508430	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35624856	0.88[ASN][1000 genomes]
rs35676956	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35821254	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35851021	0.88[ASN][1000 genomes]
rs35876551	0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36059333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457208	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849324	0.91[ASN][1000 genomes]
rs55889925	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006261	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56235846	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56675463	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs59308022	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs60201031	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60326618	0.90[AFR][1000 genomes]
rs66510832	0.83[ASN][1000 genomes]
rs67319329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71535634	0.85[ASN][1000 genomes]
rs71535635	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs71563136	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs869249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13238478	ZNF117	cis	parietal	SCAN
rs13238478	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13238478	CRCP	cis	parietal	SCAN
rs13238478	ASL	cis	multi-tissue	Pritchard
rs13238478	GUSB	cis	Whole Blood	GTEx
rs13238478	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13238478	RP4-756H11.3	cis	lung	GTEx
rs13238478	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs13238478	ZNF117	cis	cerebellum	SCAN
rs13238478	ZNF273	cis	parietal	SCAN
rs13238478	VKORC1L1	cis	parietal	SCAN
rs13238478	CRCP	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66385400-66388200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr7:66386200-66388200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:66387000-66388200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:66387000-66388600	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr7:66387200-66388200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:66387200-66388400	Flanking Active TSS	Dnd41	blood
7	chr7:66387200-66388800	Enhancers	Spleen	Spleen
8	chr7:66387400-66388200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:66387400-66388200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr7:66387400-66388400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:66387400-66389400	Enhancers	Small Intestine	intestine
12	chr7:66387400-66395000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:66387400-66395000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:66387600-66388200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:66387600-66388200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:66387600-66388200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr7:66387600-66388200	Enhancers	Fetal Muscle Leg	muscle
18	chr7:66387600-66388200	Weak transcription	Gastric	stomach
19	chr7:66387600-66388200	Weak transcription	Left Ventricle	heart
20	chr7:66387600-66388400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:66387600-66388400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr7:66387600-66388400	Enhancers	Primary B cells from peripheral blood	blood
23	chr7:66387600-66388400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr7:66387600-66388400	Enhancers	Brain Germinal Matrix	brain
25	chr7:66387600-66388400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:66387600-66388400	Weak transcription	Brain Substantia Nigra	brain
27	chr7:66387600-66388400	Enhancers	Colonic Mucosa	Colon
28	chr7:66387600-66388400	Weak transcription	Fetal Intestine Large	intestine
29	chr7:66387600-66388400	Enhancers	Fetal Lung	lung
30	chr7:66387600-66388400	Weak transcription	Ovary	ovary
31	chr7:66387600-66388400	Weak transcription	Right Atrium	heart
32	chr7:66387600-66388400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr7:66387600-66388600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:66387600-66388600	Enhancers	Brain Angular Gyrus	brain
35	chr7:66387600-66388600	Enhancers	Brain Cingulate Gyrus	brain
36	chr7:66387600-66388600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr7:66387600-66388600	Enhancers	Placenta	Placenta
38	chr7:66387600-66388600	Enhancers	Lung	lung
39	chr7:66387600-66388600	Enhancers	Psoas Muscle	Psoas
40	chr7:66387600-66388800	Genic enhancers	Fetal Stomach	stomach
41	chr7:66387600-66389000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr7:66387600-66389000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:66387600-66389000	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr7:66387600-66389000	Enhancers	Fetal Brain Male	brain
45	chr7:66387600-66389000	Enhancers	Pancreas	Pancrea
46	chr7:66387600-66389000	Enhancers	Right Ventricle	heart
47	chr7:66387600-66389200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr7:66387600-66389200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr7:66387600-66389200	Enhancers	Liver	Liver
50	chr7:66387600-66389200	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links