Variant report

Variant	rs10005702
Chromosome Location	chr4:172849152-172849153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:172844152..172846953-chr4:172848968..172851507,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10009436	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10032268	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs11935161	0.97[EUR][1000 genomes]
rs12508478	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13118856	0.82[EUR][1000 genomes]
rs13152268	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs1485872	0.81[CEU][hapmap]
rs17057754	0.81[CEU][hapmap]
rs2002564	0.98[EUR][1000 genomes]
rs231586	0.89[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap]
rs2332433	0.81[EUR][1000 genomes]
rs2332434	0.81[EUR][1000 genomes]
rs2877676	0.81[EUR][1000 genomes]
rs332962	0.84[CEU][hapmap]
rs332981	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs333003	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs333004	0.92[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap]
rs333008	0.89[EUR][1000 genomes]
rs373772	0.81[EUR][1000 genomes]
rs392614	0.81[CEU][hapmap]
rs405831	0.81[CEU][hapmap]
rs408196	0.81[EUR][1000 genomes]
rs414428	0.81[EUR][1000 genomes]
rs4505786	1.00[LWK][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs4692643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs578496	0.81[EUR][1000 genomes]
rs6553602	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6840431	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855295	0.89[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs693756	0.81[EUR][1000 genomes]
rs7434835	0.82[EUR][1000 genomes]
rs7674002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875802	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv881602	chr4:172772005-172867912	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv870367	chr4:172834672-172867495	Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv1018930	chr4:172836503-172865509	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv519578	chr4:172842419-172858612	Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10005702	GALNTL6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:172846200-172850600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:172846400-172849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:172848200-172851400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links