Variant report

Variant	rs13004227
Chromosome Location	chr2:77712840-77712841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10177313	0.84[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap]
rs10182084	0.84[CHB][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10183593	0.84[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap]
rs10185975	0.83[CHB][hapmap]
rs10189992	0.83[CHB][hapmap];0.87[YRI][hapmap]
rs10206763	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs10445951	0.87[YRI][hapmap]
rs11126609	0.81[CHB][hapmap]
rs11675925	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11679943	0.84[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap]
rs11690280	0.88[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12328979	0.81[CHB][hapmap]
rs12329320	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12477579	0.84[CEU][hapmap]
rs12621012	0.84[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs12713915	0.84[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap]
rs12713916	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13027825	0.87[ASW][hapmap];0.84[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap]
rs13029709	0.83[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap]
rs13418152	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17594976	0.84[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap]
rs1922812	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1922819	0.81[ASN][1000 genomes]
rs2204914	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2861074	0.84[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs2901851	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309596	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4542882	0.83[CHB][hapmap];0.84[JPT][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5007084	0.81[CHB][hapmap]
rs6729915	0.83[EUR][1000 genomes]
rs6740247	0.84[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.81[ASN][1000 genomes]
rs6749867	0.80[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap]
rs6761838	0.82[EUR][1000 genomes]
rs72811280	0.81[ASN][1000 genomes]
rs7564840	0.84[CHB][hapmap]
rs7587183	0.84[CHB][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874333	chr2:77315349-77798886	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv518504	chr2:77326832-78172786	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1004938	chr2:77347740-78186543	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535783	chr2:77347740-78186543	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529904	chr2:77347741-78186542	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv997329	chr2:77354560-78176285	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv520560	chr2:77675884-77724557	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv582257	chr2:77681802-77721110	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv874338	chr2:77683562-77747513	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv874339	chr2:77683562-77872197	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13004227	LYPD6B	trans	cerebellum	SCAN
rs13004227	REG3A	cis	parietal	SCAN
rs13004227	POLE4	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77708400-77715400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:77711400-77715400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:77712200-77714200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:77712600-77714400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links