Variant report

Variant	rs3851365
Chromosome Location	chr3:160191236-160191237
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:160191200-160191350	HAc	cerebellar:	n/a	n/a
2	FOSL2	chr3:160191012-160192665	SK-N-SH	brain:	n/a	chr3:160191282-160191292 chr3:160191282-160191292 chr3:160191282-160191292 chr3:160191282-160191292 chr3:160191282-160191291
3	CTCF	chr3:160191220-160191370	BJ	skin:	n/a	n/a
4	CTCF	chr3:160191220-160191370	AG04450	lung:	n/a	n/a
5	NFIC	chr3:160190976-160193068	SK-N-SH	brain:	n/a	chr3:160192549-160192577 chr3:160192454-160192471
6	TCF12	chr3:160190943-160192899	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr3:160191160-160191310	HA-sp	spinal cord:	n/a	n/a
8	ELK1	chr3:160191236-160191253	Hela-S3	cervix:	n/a	n/a
9	TCF12	chr3:160190823-160193016	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160184913..160186500-chr3:160191059..160193425,2	K562	blood:

Variant related genes	Relation type
RNU7-136P	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1047210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10513551	0.85[CEU][hapmap]
rs10936203	0.81[JPT][hapmap]
rs11706810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11718121	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12632030	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13403	0.85[CEU][hapmap]
rs1369666	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1451760	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1451761	0.85[CEU][hapmap]
rs1451762	0.85[CEU][hapmap]
rs17236473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17236544	0.81[CEU][hapmap];0.80[GIH][hapmap]
rs17570467	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs17826221	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17826257	0.81[JPT][hapmap]
rs1882126	0.81[CEU][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs1882127	0.81[CEU][hapmap]
rs1920642	0.81[CEU][hapmap]
rs1920664	0.81[CEU][hapmap]
rs1953506	0.85[CEU][hapmap]
rs1971128	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2123003	0.85[ASN][1000 genomes]
rs2279457	0.85[CEU][hapmap]
rs2305407	0.87[CEU][hapmap]
rs3732706	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3773372	0.81[CEU][hapmap]
rs3851366	0.85[CEU][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes]
rs4091703	0.81[AMR][1000 genomes]
rs4679654	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679881	0.85[CEU][hapmap]
rs4679885	0.85[CEU][hapmap]
rs4679890	0.80[CEU][hapmap]
rs4679891	0.80[CEU][hapmap]
rs4679895	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679899	0.81[CEU][hapmap]
rs4680576	0.85[CEU][hapmap]
rs4680579	0.85[CEU][hapmap]
rs4680580	0.85[CEU][hapmap]
rs4680585	0.85[CEU][hapmap]
rs4680588	0.85[CEU][hapmap]
rs4680589	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680591	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55992947	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56156703	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56394279	0.83[AMR][1000 genomes]
rs6441313	0.85[CEU][hapmap]
rs6441314	0.85[CEU][hapmap]
rs6441319	0.81[CEU][hapmap]
rs6441320	0.85[CEU][hapmap]
rs6441324	0.81[CEU][hapmap]
rs6768975	0.81[CEU][hapmap]
rs6785881	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6790951	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6791056	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6791261	0.85[CEU][hapmap]
rs6793560	0.88[CEU][hapmap]
rs6798183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6798668	0.81[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs6803828	0.85[CEU][hapmap]
rs6808083	0.88[JPT][hapmap]
rs6809153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7355951	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7611130	0.85[CEU][hapmap]
rs7618974	0.81[CEU][hapmap]
rs7620828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7621724	0.81[CEU][hapmap]
rs7624902	0.85[CEU][hapmap]
rs7627555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7627756	0.81[CEU][hapmap]
rs7629	0.85[CEU][hapmap]
rs7631792	0.85[CEU][hapmap]
rs7634108	0.84[CEU][hapmap]
rs7634826	0.85[CEU][hapmap];0.88[JPT][hapmap]
rs7640072	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs7643779	0.81[CEU][hapmap]
rs7647873	0.81[CEU][hapmap]
rs869467	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs869468	0.85[CEU][hapmap]
rs9968151	0.85[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3851365	IFT80	cis	parietal	SCAN
rs3851365	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs3851365	NMD3	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160189800-160191400	Enhancers	NH-A	brain
2	chr3:160189800-160193400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:160189800-160193400	Enhancers	HMEC	breast
4	chr3:160190200-160191400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:160190200-160191400	Enhancers	NHDF-Ad	bronchial
6	chr3:160190200-160191400	Enhancers	Osteobl	bone
7	chr3:160190200-160192400	Enhancers	HSMMtube	muscle
8	chr3:160190200-160192800	Enhancers	HSMM	muscle
9	chr3:160190200-160193000	Enhancers	NHLF	lung
10	chr3:160190200-160193400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:160190200-160194200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:160190400-160192200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:160190400-160193000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:160190400-160193200	Enhancers	NHEK	skin
15	chr3:160190600-160191800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:160190600-160199600	Weak transcription	Brain Substantia Nigra	brain
17	chr3:160191000-160192200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:160191000-160193000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:160191200-160191600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:160191200-160192600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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