Variant report

Variant	rs7654770
Chromosome Location	chr4:48489267-48489268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:48489221-48489271	HUVEC	blood vessel:	n/a
2	chr4:48489221-48489271	A549	lung:	n/a
3	chr4:48489221-48489271	NHBE	bronchial:	n/a
4	chr4:48489221-48489271	BJ	skin:	n/a
5	chr4:48489221-48489271	MCF10A-Er-Src	breast:	n/a
6	chr4:48489221-48489271	MCF-7	breast:	n/a
7	chr4:48489221-48489271	HIPEpiC	eye:	n/a
8	chr4:48489221-48489271	Jurkat	blood:	n/a
9	chr4:48489221-48489271	HRCEpiC	kidney:	n/a
10	chr4:48489221-48489271	HL-60	blood:	n/a
11	chr4:48489221-48489271	Hepatocyte	liver:	n/a
12	chr4:48489221-48489271	BE2_C	brain:	n/a
13	chr4:48489221-48489271	GM12892	blood:	n/a
14	chr4:48489221-48489271	SAEC	small airway:	n/a
15	chr4:48489221-48489271	GM06990	blood:	n/a
16	chr4:48489221-48489271	AG09319	gingival:	n/a
17	chr4:48489221-48489271	HCT-116	colon:	n/a
18	chr4:48489221-48489271	GM12878	blood:	n/a
19	chr4:48489221-48489271	HepG2	liver:	n/a
20	chr4:48489221-48489271	HCM	heart:	n/a
21	chr4:48489221-48489271	HCPEpiC	choroid plexus:	n/a
22	chr4:48489221-48489271	IMR90	lung:	fetal
23	chr4:48489221-48489271	AoSMC	blood vessel:	n/a
24	chr4:48489221-48489271	HEEpiC	esophagus:	n/a
25	chr4:48489221-48489271	PANC-1	pancreas:	n/a
26	chr4:48489221-48489271	AG09309	skin:	n/a
27	chr4:48489221-48489271	HEK293	kidney:	embryo
28	chr4:48489221-48489271	H1-hESC	embryonic stem cell:	embryo
29	chr4:48489221-48489271	ProgFib	skin:	n/a
30	chr4:48489221-48489271	AG04449	skin:	fetal
31	chr4:48489221-48489271	HNPCEpiC	eye:	n/a
32	chr4:48489221-48489271	CMK	blood:	n/a
33	chr4:48489221-48489271	Hela-S3	cervix:	n/a
34	chr4:48489221-48489271	Caco-2	colon:	n/a
35	chr4:48489221-48489271	HMEC	breast:	n/a
36	chr4:48489221-48489271	HCF	heart:	n/a
37	chr4:48489221-48489271	PFSK-1	brain:	n/a
38	chr4:48489221-48489271	NB4	blood:	n/a
39	chr4:48489221-48489271	ECC-1	luminal epithelium:	n/a
40	chr4:48489221-48489271	GM12891	blood:	n/a
41	chr4:48489221-48489271	NT2-D1	testis:	n/a
42	chr4:48489221-48489271	HRE	kidney:	n/a
43	chr4:48489221-48489271	NHDF-neo	bronchial:	n/a
44	chr4:48489221-48489271	LNCaP	prostate:	n/a
45	chr4:48489221-48489271	HPAEpiC	pulmonary alveolar:	n/a
46	chr4:48489221-48489271	GM19239	blood:	n/a
47	chr4:48489221-48489271	NH-A	brain:	n/a
48	chr4:48489221-48489271	AG10803	skin:	n/a
49	chr4:48489221-48489271	U87	brain:	n/a
50	chr4:48489221-48489271	ovcar-3	ovarian:	n/a

No data

Variant related genes	Relation type
ZAR1	CpG island

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10018344	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10029732	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10029785	0.86[JPT][hapmap]
rs10030853	0.86[EUR][1000 genomes]
rs10031777	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10049761	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs10938534	0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10938537	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11734019	0.84[EUR][1000 genomes]
rs11737677	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs11933919	0.86[EUR][1000 genomes]
rs11945562	0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12503599	0.86[EUR][1000 genomes]
rs12506098	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12645501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645951	0.86[JPT][hapmap]
rs13108474	0.84[EUR][1000 genomes]
rs13119041	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs13127730	0.85[EUR][1000 genomes]
rs13138269	0.84[EUR][1000 genomes]
rs1472967	0.86[JPT][hapmap]
rs1507862	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1507865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1702798	0.83[EUR][1000 genomes]
rs1712767	0.81[EUR][1000 genomes]
rs1712768	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1712772	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17575720	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs17656010	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17656040	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17656076	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17656094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1876469	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs2089503	0.85[EUR][1000 genomes]
rs2102397	0.87[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap]
rs2291474	0.86[JPT][hapmap]
rs2291475	0.86[JPT][hapmap]
rs2354348	0.87[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.85[EUR][1000 genomes]
rs28470767	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs28733443	0.81[EUR][1000 genomes]
rs2940324	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2945330	0.91[EUR][1000 genomes]
rs3107022	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34558821	0.86[EUR][1000 genomes]
rs34635008	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs392187	0.86[JPT][hapmap]
rs404445	0.86[JPT][hapmap]
rs411261	0.86[JPT][hapmap]
rs421833	0.86[JPT][hapmap]
rs4536901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4695391	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59686413	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62311296	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447640	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447645	0.86[EUR][1000 genomes]
rs6447647	0.86[EUR][1000 genomes]
rs6811148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816010	0.86[JPT][hapmap]
rs6819159	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6821277	0.86[JPT][hapmap]
rs6829144	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6829716	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6836632	0.86[ASW][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6838613	0.82[EUR][1000 genomes]
rs6843340	0.83[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs6848073	0.91[JPT][hapmap]
rs6855022	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6856448	0.86[EUR][1000 genomes]
rs7438704	0.85[JPT][hapmap]
rs7661515	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7667288	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs7678379	0.87[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679210	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7683398	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs7693461	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7697851	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs776584	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs776588	0.80[EUR][1000 genomes]
rs776590	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs776591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs776601	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs796555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs937888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs937889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs952289	0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs9884546	0.84[EUR][1000 genomes]
rs992423	0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7654770	OCIAD2	cis	lymphoblastoid	seeQTL
rs7654770	OCIAD2	cis	cerebellum	SCAN
rs7654770	SLC10A4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48485200-48490200	Active TSS	Cortex derived primary cultured neurospheres	brain
2	chr4:48486200-48492000	Weak transcription	Aorta	Aorta
3	chr4:48486600-48491800	Weak transcription	Pancreas	Pancrea
4	chr4:48487200-48505800	Weak transcription	A549	lung
5	chr4:48489200-48489400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
6	chr4:48489200-48489400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
7	chr4:48489200-48489600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr4:48489200-48489600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:48489200-48490400	Strong transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links