Variant report

Variant	rs1404613
Chromosome Location	chr7:14726723-14726724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10228891	0.93[CHD][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs10259838	0.94[CHD][hapmap];0.83[MEX][hapmap]
rs10262035	0.98[EUR][1000 genomes]
rs10279650	0.82[CHB][hapmap]
rs10279786	0.82[CHB][hapmap]
rs10499462	0.87[CHD][hapmap]
rs11971649	0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs12537147	0.81[CEU][hapmap]
rs12539208	0.84[AMR][1000 genomes]
rs12669997	0.85[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs12699654	0.89[CEU][hapmap];0.94[CHD][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12699655	0.89[CEU][hapmap];0.94[CHD][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12699658	0.85[GIH][hapmap]
rs1357856	0.83[AMR][1000 genomes]
rs1357860	0.82[CHB][hapmap]
rs1357861	0.96[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1357862	0.87[EUR][1000 genomes]
rs1357863	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1357872	0.81[CEU][hapmap]
rs1404614	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs1404615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525078	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1525099	0.82[CHD][hapmap];0.82[AMR][1000 genomes]
rs1568843	0.82[CHB][hapmap]
rs1568844	0.82[CHB][hapmap]
rs1568846	0.85[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs1568847	0.81[CEU][hapmap];0.87[CHD][hapmap];0.81[AMR][1000 genomes]
rs17668635	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17668761	0.84[AMR][1000 genomes]
rs1997040	0.81[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs2293339	1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs2358025	0.82[CHB][hapmap]
rs4027159	0.82[CHB][hapmap]
rs4236282	0.82[CHB][hapmap]
rs4424153	0.82[CHB][hapmap]
rs4521664	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4719417	0.81[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs6461120	0.87[CHD][hapmap]
rs6944222	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6947566	0.87[CHD][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs6954517	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs6956435	0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6956606	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6965637	0.81[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs6966274	0.81[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs7784799	0.82[AMR][1000 genomes]
rs7785767	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs7791900	1.00[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs7793583	0.82[CHB][hapmap]
rs7801612	0.82[CHB][hapmap]
rs885438	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639210	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9639212	0.87[CHD][hapmap]
rs9639213	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9784967	0.83[AMR][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	nsv949033	chr7:14086106-14860323	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1031041	chr7:14624127-14999201	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538741	chr7:14624127-14999201	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1015777	chr7:14661754-14730811	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv887712	chr7:14717872-14829858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1404613	DGKB	cis	cerebellum	SCAN
rs1404613	ASTL	trans	cerebellum	SCAN
rs1404613	DGKB	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14704200-14736000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:14712800-14775200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:14720800-14728400	Weak transcription	Brain Angular Gyrus	brain
4	chr7:14722400-14726800	Weak transcription	Osteobl	bone
5	chr7:14725400-14727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:14725600-14727600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:14726600-14727000	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links