Variant report

Variant	rs17591266
Chromosome Location	chr13:40357677-40357678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:40357398..40357912-chr13:41255037..41255911,2	MCF-7	breast:
2	chr13:40356408..40358571-chr13:40377020..40378591,2	MCF-7	breast:
3	chr13:40356532..40358083-chr13:40516675..40517859,10	MCF-7	breast:
4	chr13:40357238..40358196-chr13:40516595..40517557,4	MCF-7	breast:
5	chr13:40349745..40352056-chr13:40357324..40359153,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11147769	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17591231	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3812882	0.87[JPT][hapmap]
rs3812883	0.87[JPT][hapmap]
rs3812884	0.87[JPT][hapmap]
rs3812885	0.87[JPT][hapmap]
rs3812886	0.87[JPT][hapmap]
rs3812887	0.87[JPT][hapmap]
rs3812888	0.87[JPT][hapmap]
rs4133063	0.80[LWK][hapmap]
rs4142370	0.87[JPT][hapmap]
rs4245396	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4312180	0.83[JPT][hapmap]
rs4338665	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4403927	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4408422	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4409964	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4941936	0.95[JPT][hapmap]
rs4941937	0.86[JPT][hapmap]
rs4941938	0.86[JPT][hapmap]
rs4941939	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs4941941	0.83[JPT][hapmap]
rs4943686	0.87[JPT][hapmap]
rs4943694	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4943695	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4943696	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7319128	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7325068	0.91[CEU][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7325655	0.87[JPT][hapmap]
rs7327779	0.87[JPT][hapmap]
rs7327824	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7332791	0.80[JPT][hapmap]
rs7334651	0.91[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7337585	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7984113	0.87[JPT][hapmap]
rs7998641	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8181861	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9315720	0.87[JPT][hapmap]
rs9315725	0.82[JPT][hapmap]
rs9315729	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9315730	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9532408	0.86[JPT][hapmap]
rs9532411	0.85[JPT][hapmap]
rs9532412	0.87[JPT][hapmap]
rs9532420	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs9532429	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9532432	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9532433	0.84[AFR][1000 genomes]
rs9532434	0.83[AFR][1000 genomes]
rs9532436	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9532439	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548857	0.87[JPT][hapmap]
rs9548859	0.87[JPT][hapmap]
rs9548862	0.86[JPT][hapmap]
rs9548863	0.86[JPT][hapmap]
rs9548865	0.87[JPT][hapmap]
rs9548866	0.87[JPT][hapmap]
rs9548867	0.87[JPT][hapmap]
rs9548868	0.87[JPT][hapmap]
rs9548869	0.87[JPT][hapmap]
rs9548875	0.83[JPT][hapmap]
rs9548880	0.83[JPT][hapmap]
rs9548900	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9548901	0.91[CEU][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9548916	0.90[CEU][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9548917	0.91[CEU][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9548918	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9548919	0.91[CEU][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9548920	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9548926	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548928	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9548929	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548930	0.91[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9548932	0.84[AFR][1000 genomes]
rs9566474	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9576881	0.87[JPT][hapmap]
rs9576882	0.87[JPT][hapmap]
rs9576891	0.83[EUR][1000 genomes]
rs9576892	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9576896	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9576897	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9576898	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9603617	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17591266	COG6	cis	Muscle Skeletal	GTEx
rs17591266	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
2	chr13:40342600-40360200	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:40351800-40358400	Weak transcription	Ovary	ovary
4	chr13:40351800-40360200	Weak transcription	Left Ventricle	heart
5	chr13:40352000-40361400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr13:40353800-40358000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr13:40353800-40358400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:40353800-40360000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:40354000-40358200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:40354000-40358800	Weak transcription	NHLF	lung
11	chr13:40354000-40363200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:40354400-40358200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr13:40354400-40358400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr13:40354600-40358200	Weak transcription	Osteobl	bone
15	chr13:40354600-40360200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:40355400-40358200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:40356000-40360200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr13:40356400-40360800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:40357000-40360200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:40357200-40358200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:40357400-40360000	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links