Variant report

Variant	rs7690646
Chromosome Location	chr4:172868945-172868946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10031122	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10866351	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11931247	1.00[CEU][hapmap];0.91[MEX][hapmap];0.87[EUR][1000 genomes]
rs13106824	1.00[CEU][hapmap]
rs13111782	0.87[EUR][1000 genomes]
rs13130415	0.82[CEU][hapmap]
rs1385794	0.88[EUR][1000 genomes]
rs1485863	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1485867	0.82[CEU][hapmap]
rs179641	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs189146	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs3113678	0.90[YRI][hapmap]
rs332980	0.88[EUR][1000 genomes]
rs332982	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs332983	1.00[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs332992	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs332993	0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap]
rs332995	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs332996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs333002	0.93[CEU][hapmap]
rs405831	0.83[YRI][hapmap]
rs453429	0.90[YRI][hapmap]
rs6553603	0.94[CEU][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs6818985	0.82[CEU][hapmap]
rs6825635	0.82[CEU][hapmap]
rs6832294	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6839553	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs6845054	1.00[CEU][hapmap];0.84[MEX][hapmap]
rs6854192	0.82[CEU][hapmap]
rs72985392	0.87[EUR][1000 genomes]
rs7666494	0.94[CEU][hapmap]
rs875801	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9998139	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022527	chr4:172547732-173236939	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537357	chr4:172547732-173236939	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1024693	chr4:172609237-173236939	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv596197	chr4:172797761-172868945	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv520744	chr4:172797761-172897603	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1029351	chr4:172809594-172893072	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv498033	chr4:172830955-173121438	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7690646	HMGB2	cis	cerebellum	SCAN
rs7690646	GALNTL6	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:172867600-172869000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:172868000-172869000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:172868200-172869600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr4:172868400-172869000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:172868400-172869000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr4:172868400-172869000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr4:172868400-172869000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:172868400-172869600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:172868400-172869800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:172868600-172869000	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links