Variant report

Variant	rs12939390
Chromosome Location	chr17:28635688-28635689
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	chr17:28634091..28636614-chr17:28804308..28805890,2	K562	blood:

Variant related genes	Relation type
ENSG00000108587	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1050565	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11656408	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11867581	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs11870192	0.82[AMR][1000 genomes]
rs12938714	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12941223	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945042	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12947654	0.84[EUR][1000 genomes]
rs12949747	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13341611	0.94[JPT][hapmap]
rs1487971	0.84[CEU][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap]
rs17767256	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2321706	0.91[ASN][1000 genomes]
rs3103303	0.93[ASN][1000 genomes]
rs3103306	0.91[ASN][1000 genomes]
rs3110060	0.87[ASN][1000 genomes]
rs3110061	0.87[ASN][1000 genomes]
rs3110452	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs3110454	0.87[ASN][1000 genomes]
rs33980254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34353378	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34622227	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35724800	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36000555	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36048853	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794806	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816828	0.94[JPT][hapmap]
rs6505165	0.94[JPT][hapmap]
rs6505169	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs6505173	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7208052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7210085	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7214014	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7214248	0.95[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7214991	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap]
rs7215330	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap]
rs7223821	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73268099	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7342921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7342929	0.94[JPT][hapmap]
rs8072345	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs8078900	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8080149	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998087	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064975	chr17:28604187-28851905	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv543299	chr17:28604187-28851905	Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv543300	chr17:28620420-28659310	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12939390	GOSR1	cis	parietal	SCAN
rs12939390	BLMH	Cis_1M	lymphoblastoid	RTeQTL
rs12939390	CPD	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:28634000-28636800	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr17:28635000-28636000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:28635000-28636200	Enhancers	Fetal Intestine Small	intestine
4	chr17:28635200-28636600	Enhancers	Fetal Intestine Large	intestine
5	chr17:28635600-28636000	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links