Variant report

Variant	rs6798668
Chromosome Location	chr3:160200408-160200409
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160197463..160200948-chr3:160202172..160205556,5	K562	blood:
2	chr3:160193260..160196104-chr3:160198716..160201117,2	K562	blood:
3	chr3:160200027..160203201-chr3:160206463..160209183,3	MCF-7	breast:
4	chr3:160198112..160200479-chr3:160205569..160207297,2	K562	blood:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10212236	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1047210	0.81[CEU][hapmap]
rs10513551	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11706810	0.81[CEU][hapmap]
rs11918749	0.83[EUR][1000 genomes]
rs1317365	0.88[CEU][hapmap]
rs13403	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1451761	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1451762	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1451764	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1551190	0.80[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1584688	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17236473	0.81[CEU][hapmap]
rs17236544	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs17570467	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17826221	0.81[CEU][hapmap]
rs1882126	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1882127	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes]
rs1920642	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs1920657	0.83[JPT][hapmap]
rs1920662	0.87[EUR][1000 genomes]
rs1920664	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs1953506	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1971128	0.80[ASN][1000 genomes]
rs2152425	0.88[CEU][hapmap]
rs2279457	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305407	0.95[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs2366969	0.82[EUR][1000 genomes]
rs28705750	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2886825	0.86[EUR][1000 genomes]
rs3732706	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs3732707	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3773372	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3851365	0.81[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs3851366	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4091703	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4292273	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4292274	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4621370	0.85[EUR][1000 genomes]
rs4679654	0.84[AMR][1000 genomes]
rs4679655	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4679881	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs4679885	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4679888	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679889	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679890	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4679891	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4679896	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4679899	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs4679900	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680576	0.96[CEU][hapmap]
rs4680579	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs4680580	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4680585	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680587	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680588	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680589	0.80[ASN][1000 genomes]
rs4680591	0.86[AMR][1000 genomes]
rs55731730	0.82[EUR][1000 genomes]
rs56197102	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56394279	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58322641	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58665246	0.82[EUR][1000 genomes]
rs60009222	0.83[EUR][1000 genomes]
rs60460891	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272186	0.82[EUR][1000 genomes]
rs62272791	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62272792	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62272794	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272800	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272810	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441313	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6441314	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6441319	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6441320	0.96[CEU][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6441324	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs6768975	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs6791261	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs6793560	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6798183	0.81[CEU][hapmap]
rs6801300	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs6803828	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6806505	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6808083	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809153	0.81[CEU][hapmap]
rs6809313	0.84[CEU][hapmap]
rs721022	0.88[CEU][hapmap]
rs721023	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73154592	0.83[EUR][1000 genomes]
rs7611130	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7618974	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7621724	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7624902	0.96[CEU][hapmap]
rs7627555	0.81[CEU][hapmap]
rs7627749	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7627756	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7629	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7629202	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7631792	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7634108	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7634826	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640072	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7643779	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7644453	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7645832	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7647873	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs869468	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9798898	0.83[EUR][1000 genomes]
rs9862595	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs9968151	0.96[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6798668	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160193400-160213000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:160195800-160203600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:160196000-160203000	Weak transcription	NHDF-Ad	bronchial
4	chr3:160196200-160203800	Weak transcription	NH-A	brain
5	chr3:160196200-160203800	Weak transcription	NHLF	lung
6	chr3:160196400-160200600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:160196400-160203000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:160196400-160203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:160197800-160203000	Weak transcription	Osteobl	bone
10	chr3:160199000-160211600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:160199600-160200800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:160199600-160201000	Enhancers	Brain Substantia Nigra	brain
13	chr3:160199600-160201800	Enhancers	Brain Anterior Caudate	brain
14	chr3:160199800-160200800	Enhancers	Brain Angular Gyrus	brain
15	chr3:160200000-160200800	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:160200000-160202400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:160200000-160203200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:160200400-160203200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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