Variant report

Variant	rs6803889
Chromosome Location	chr3:177406064-177406065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:177398506..177400476-chr3:177405856..177408346,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10513747	0.82[ASN][1000 genomes]
rs10513748	1.00[ASN][1000 genomes]
rs10513749	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10513750	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936953	0.94[CHB][hapmap]
rs10936954	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487458	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489304	0.81[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12490852	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12496321	0.86[ASN][1000 genomes]
rs13059117	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059514	0.94[CHB][hapmap]
rs13060224	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13060502	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13074455	0.84[ASN][1000 genomes]
rs13082519	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13097723	0.94[ASN][1000 genomes]
rs13340118	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13340167	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13340172	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1499809	0.86[ASN][1000 genomes]
rs1499810	0.95[ASN][1000 genomes]
rs1499811	0.81[ASN][1000 genomes]
rs1500047	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1500048	0.84[ASN][1000 genomes]
rs1604032	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17635512	0.86[ASN][1000 genomes]
rs17635597	0.84[ASN][1000 genomes]
rs1846628	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2062499	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2062500	0.94[CHB][hapmap]
rs28700961	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28711160	0.92[ASN][1000 genomes]
rs33964414	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34066617	0.84[ASN][1000 genomes]
rs34188001	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34347103	0.84[ASN][1000 genomes]
rs34407557	0.86[ASN][1000 genomes]
rs34557886	0.86[ASN][1000 genomes]
rs34638059	0.86[ASN][1000 genomes]
rs34763113	0.86[ASN][1000 genomes]
rs34992356	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35110045	0.86[ASN][1000 genomes]
rs35468531	0.84[ASN][1000 genomes]
rs35610650	0.86[ASN][1000 genomes]
rs35652846	0.86[ASN][1000 genomes]
rs35791913	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35830472	0.84[ASN][1000 genomes]
rs35868955	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36055300	0.86[ASN][1000 genomes]
rs4857725	0.94[ASN][1000 genomes]
rs4857726	0.94[ASN][1000 genomes]
rs57405296	0.89[ASN][1000 genomes]
rs61541774	0.86[ASN][1000 genomes]
rs62283347	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6443481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443482	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66636257	0.86[ASN][1000 genomes]
rs67189039	0.86[ASN][1000 genomes]
rs6765836	0.94[ASN][1000 genomes]
rs6772134	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6779492	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67797381	0.86[ASN][1000 genomes]
rs6793629	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6793647	0.92[ASN][1000 genomes]
rs6798785	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71308158	0.86[ASN][1000 genomes]
rs7610506	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7615900	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639373	0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7641099	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7644248	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7646117	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7652174	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937507	1.00[ASN][1000 genomes]
rs937561	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv998537	chr3:177403421-177425648	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1009087	chr3:177405231-177422275	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6803889	KCNMB2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:177398800-177421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:177400400-177406200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:177405200-177407000	Enhancers	Brain Hippocampus Middle	brain
6	chr3:177405400-177406800	Enhancers	Brain Anterior Caudate	brain
7	chr3:177405400-177406800	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:177405400-177406800	Enhancers	Brain Substantia Nigra	brain
9	chr3:177405600-177406200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:177405600-177411400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:177405800-177406400	Enhancers	Brain Germinal Matrix	brain
12	chr3:177405800-177406600	Enhancers	Colon Smooth Muscle	Colon
13	chr3:177405800-177411600	Weak transcription	Fetal Brain Male	brain
14	chr3:177406000-177406200	Enhancers	Brain Angular Gyrus	brain
15	chr3:177406000-177406400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr3:177406000-177406600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:177406000-177406600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:177406000-177407000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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