Variant report

Variant	rs6789496
Chromosome Location	chr3:158883984-158883985
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12635142	0.95[JPT][hapmap]
rs1375407	1.00[JPT][hapmap]
rs1449027	0.82[CHB][hapmap]
rs1562672	0.82[CHB][hapmap]
rs17795566	0.82[CHB][hapmap]
rs1900861	1.00[JPT][hapmap]
rs1975601	0.82[CHB][hapmap]
rs2365478	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2595232	0.82[CHB][hapmap]
rs2595236	0.82[CHB][hapmap]
rs2595242	0.82[CHB][hapmap]
rs2595243	0.82[CHB][hapmap]
rs2595244	0.82[CHB][hapmap]
rs2595245	0.82[CHB][hapmap]
rs2595246	0.80[CHB][hapmap]
rs2595258	0.95[JPT][hapmap]
rs2621277	0.95[JPT][hapmap]
rs2621284	0.86[CHB][hapmap]
rs2621292	0.95[JPT][hapmap]
rs2621294	0.82[CHB][hapmap]
rs2621295	0.82[CHB][hapmap]
rs2621297	0.82[CHB][hapmap]
rs2621299	0.82[CHB][hapmap]
rs2621300	0.81[CHB][hapmap]
rs2621306	0.82[CHB][hapmap]
rs4020070	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4296631	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4501157	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4645169	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680494	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680495	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6788475	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6805303	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7634829	1.00[JPT][hapmap]
rs9848481	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs9879667	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3426016	chr3:158676623-158979242	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv491927	chr3:158692653-158952780	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1010828	chr3:158802474-158894319	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158881800-158886600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:158881800-158886600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:158881800-158886600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:158881800-158886600	Weak transcription	HMEC	breast
5	chr3:158882000-158887400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:158882200-158884000	Weak transcription	Stomach Mucosa	stomach
7	chr3:158882200-158887400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:158882200-158887400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:158882400-158887400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:158882600-158886600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:158882800-158884400	Enhancers	Fetal Brain Female	brain
12	chr3:158882800-158887400	Weak transcription	A549	lung
13	chr3:158883600-158884600	Enhancers	HUVEC	blood vessel
14	chr3:158883800-158884000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr3:158883800-158884400	Enhancers	Brain Cingulate Gyrus	brain

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