Variant report

Variant	rs807932
Chromosome Location	chr3:47354241-47354242
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47314259..47316473-chr3:47352261..47355083,2	K562	blood:
2	chr3:47326087..47329023-chr3:47353816..47355413,2	K562	blood:
3	chr3:47346723..47349311-chr3:47352189..47354716,2	K562	blood:
4	chr3:47346467..47349928-chr3:47352016..47354716,3	K562	blood:
5	chr3:47322558..47324268-chr3:47353652..47355333,2	K562	blood:
6	chr3:47328553..47330784-chr3:47354135..47356276,2	K562	blood:
7	chr3:47195998..47198423-chr3:47353673..47355758,2	K562	blood:
8	chr3:47293290..47295521-chr3:47352097..47355048,2	K562	blood:
9	chr3:47351807..47354285-chr3:47356422..47359102,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1038394	0.92[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs1076394	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865946	0.92[CEU][hapmap];0.94[YRI][hapmap]
rs11130115	0.85[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs11130123	0.85[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130124	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130126	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs11130128	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs11130129	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs11705957	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs11710013	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710121	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11710322	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711824	0.92[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap]
rs11712445	0.91[CEU][hapmap];0.95[YRI][hapmap]
rs11714294	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11716763	0.92[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11719877	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs11720439	0.80[EUR][1000 genomes]
rs11915074	0.88[CEU][hapmap]
rs11920853	0.88[CEU][hapmap]
rs12495169	0.85[JPT][hapmap]
rs12636851	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs13059519	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs13072802	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075233	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs13094438	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs1531875	0.92[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap]
rs1638676	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.81[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs17476234	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17784882	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs1872164	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs2101247	0.88[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2132173	0.85[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs2159400	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs2276853	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap]
rs2276854	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs295428	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs295433	1.00[YRI][hapmap]
rs295441	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295442	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295449	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs295458	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs295461	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3736177	0.91[CEU][hapmap]
rs3816779	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs4682852	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4683326	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858811	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.92[CEU][hapmap]
rs4858868	0.92[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs4858893	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.82[CEU][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap]
rs59689369	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6767907	0.89[TSI][hapmap]
rs6768221	0.88[CEU][hapmap]
rs6772670	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6780013	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs6791842	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs6792461	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs6800271	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs7636423	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7651762	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs807810	0.87[AFR][1000 genomes]
rs807935	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807936	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807937	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs811115	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878659	0.92[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs922957	0.92[CEU][hapmap]
rs9683033	0.92[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs9837343	0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs807932	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs807932	HYAL2	cis	cerebellum	SCAN
rs807932	PRKAR2A	cis	cerebellum	SCAN
rs807932	CCDC12	cis	cerebellum	SCAN
rs807932	AMIGO3	cis	cerebellum	SCAN
rs807932	RTP3	cis	lesional skin	skin_eQTL
rs807932	C3orf75	cis	cerebellum	SCAN
rs807932	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs807932	NCKIPSD	cis	cerebellum	SCAN
rs807932	SCAP	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47325600-47367600	Weak transcription	A549	lung
3	chr3:47326200-47356200	Weak transcription	Fetal Heart	heart
4	chr3:47326200-47356600	Weak transcription	NHDF-Ad	bronchial
5	chr3:47326200-47359600	Weak transcription	Fetal Lung	lung
6	chr3:47326200-47362200	Weak transcription	Gastric	stomach
7	chr3:47326200-47363200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:47326400-47364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:47326800-47356600	Weak transcription	Small Intestine	intestine
10	chr3:47328400-47364400	Weak transcription	Pancreas	Pancrea
11	chr3:47329200-47359800	Weak transcription	NHLF	lung
12	chr3:47330400-47356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:47330600-47359800	Weak transcription	Hela-S3	cervix
14	chr3:47330600-47360600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:47330800-47356600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:47330800-47361800	Weak transcription	HMEC	breast
17	chr3:47332200-47361800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:47332400-47355600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:47332600-47361000	Weak transcription	Esophagus	oesophagus
20	chr3:47332800-47361000	Weak transcription	Aorta	Aorta
21	chr3:47333000-47356400	Weak transcription	Osteobl	bone
22	chr3:47333200-47364800	Weak transcription	NH-A	brain
23	chr3:47333800-47371400	Weak transcription	Psoas Muscle	Psoas
24	chr3:47336400-47360200	Weak transcription	Thymus	Thymus
25	chr3:47337000-47356600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:47337000-47361000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:47338400-47361200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:47338600-47355600	Weak transcription	Left Ventricle	heart
29	chr3:47338600-47361200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:47338600-47369800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:47338600-47371200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:47338800-47356200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:47338800-47360200	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:47339000-47356200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:47339000-47359400	Weak transcription	Spleen	Spleen
36	chr3:47339000-47361800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:47341600-47360000	Weak transcription	Fetal Intestine Large	intestine
38	chr3:47343200-47362000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:47343800-47354800	Weak transcription	HepG2	liver
40	chr3:47344200-47355200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:47344200-47356400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:47344400-47356200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:47344400-47356200	Weak transcription	HUVEC	blood vessel
44	chr3:47344400-47362200	Weak transcription	Brain Germinal Matrix	brain
45	chr3:47344600-47356600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:47344800-47356200	Weak transcription	Liver	Liver
47	chr3:47344800-47359800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:47344800-47360200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:47344800-47360400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:47344800-47361200	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links