Variant report

Variant	rs6906468
Chromosome Location	chr6:142769386-142769387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10484733	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11155241	0.86[EUR][1000 genomes]
rs11155242	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11759653	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12189838	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190271	0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12197866	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12213892	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13198644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329705	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1329707	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17071756	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1928528	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294775	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262117	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs262120	0.85[EUR][1000 genomes]
rs262130	0.85[EUR][1000 genomes]
rs3817928	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4304190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643975	0.85[EUR][1000 genomes]
rs6570511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900087	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6900233	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901807	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903424	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6912639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922607	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6925979	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73780219	0.98[ASN][1000 genomes]
rs73780221	0.98[ASN][1000 genomes]
rs7756434	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757571	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765770	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7776356	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321870	0.81[EUR][1000 genomes]
rs9373347	0.99[EUR][1000 genomes]
rs9403386	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs984932	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6906468	SF3B5	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142738000-142774200	Weak transcription	NHEK	skin
2	chr6:142748000-142782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:142751600-142780000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:142752400-142774600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:142753600-142774000	Strong transcription	Liver	Liver
6	chr6:142754000-142772800	Strong transcription	HepG2	liver
7	chr6:142760000-142770600	Weak transcription	Lung	lung
8	chr6:142762200-142773000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:142765400-142770800	Strong transcription	Placenta	Placenta
10	chr6:142766000-142770400	Strong transcription	HUVEC	blood vessel
11	chr6:142766000-142777600	Weak transcription	HSMM	muscle
12	chr6:142766200-142772400	Weak transcription	Pancreas	Pancrea
13	chr6:142766200-142773800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:142766200-142782800	Weak transcription	NHLF	lung
15	chr6:142766400-142774000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:142766400-142778000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:142766600-142770000	Weak transcription	Fetal Stomach	stomach
18	chr6:142766800-142774800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:142768000-142771200	Weak transcription	A549	lung
20	chr6:142768000-142777400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:142768600-142769600	Strong transcription	Fetal Intestine Small	intestine
22	chr6:142768800-142769400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:142768800-142769800	Strong transcription	Fetal Lung	lung
24	chr6:142769000-142769800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:142769000-142769800	Strong transcription	Fetal Intestine Large	intestine
26	chr6:142769000-142773800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:142769200-142769600	Strong transcription	HMEC	breast
28	chr6:142769200-142769800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:142769200-142769800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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