Variant report

Variant	rs10755093
Chromosome Location	chr3:140290653-140290654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLSTN2-1	chr3:140290548-140296239	ENSG00000261179.1
2	lnc-CLSTN2-1	chr3:140290548-140294071	NONHSAT092403

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10804675	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10935386	0.89[GIH][hapmap]
rs10935387	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11714465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11924925	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11924952	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12494698	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13078522	0.87[CHB][hapmap];0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs347973	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs347975	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4683508	0.81[EUR][1000 genomes]
rs4683509	0.89[GIH][hapmap]
rs4683510	0.87[CHB][hapmap]
rs6762605	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs6775380	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6799764	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6803516	0.90[JPT][hapmap]
rs7631249	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs961554	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs9845717	0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs9851873	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv870185	chr3:140265153-140395673	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10755093	C3orf58	cis	parietal	SCAN
rs10755093	ZBTB38	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140286200-140292800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:140286200-140295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:140288200-140290800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:140288400-140290800	Weak transcription	Ovary	ovary
5	chr3:140288400-140290800	Weak transcription	Right Ventricle	heart
6	chr3:140288400-140291400	Weak transcription	HSMMtube	muscle
7	chr3:140288400-140291600	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:140288400-140291800	Weak transcription	Pancreas	Pancrea
9	chr3:140288600-140291600	Weak transcription	Liver	Liver
10	chr3:140288600-140291800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:140289000-140291800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:140290200-140290800	Weak transcription	Fetal Brain Female	brain
13	chr3:140290400-140291000	Enhancers	Brain Anterior Caudate	brain
14	chr3:140290600-140290800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:140290600-140291000	Enhancers	Colon Smooth Muscle	Colon
16	chr3:140290600-140292200	Enhancers	Right Atrium	heart
17	chr3:140290600-140293200	Enhancers	Left Ventricle	heart

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