Variant report

Variant	rs6767441
Chromosome Location	chr3:99863183-99863184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10222474	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487143	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12488245	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12629505	0.82[ASN][1000 genomes]
rs13059754	0.92[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs1387647	0.92[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2130369	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2316263	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs4928150	0.92[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs4928151	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4928153	0.92[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4928237	0.92[CEU][hapmap]
rs6440967	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6798114	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802817	0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6806323	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs720688	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7619080	0.84[ASN][1000 genomes]
rs7629487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636776	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7649349	0.92[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs766778	0.92[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs902159	0.92[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs923472	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs9289981	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814549	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837131	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849632	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865713	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6767441	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs6767441	SENP7	cis	parietal	SCAN
rs6767441	EPHX1	trans	cerebellum	SCAN
rs6767441	OR5H6	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99847000-99868800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:99855400-99868000	Weak transcription	Left Ventricle	heart
4	chr3:99856000-99868000	Weak transcription	Aorta	Aorta
5	chr3:99856000-99877800	Weak transcription	Ovary	ovary
6	chr3:99858600-99865800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:99858600-99868600	Weak transcription	Pancreas	Pancrea
8	chr3:99858600-99877200	Weak transcription	HSMM	muscle
9	chr3:99859200-99870200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:99860200-99874000	Weak transcription	A549	lung
11	chr3:99860800-99868000	Weak transcription	Fetal Stomach	stomach
12	chr3:99860800-99868400	Weak transcription	NHDF-Ad	bronchial
13	chr3:99861000-99870000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:99861400-99863200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:99861600-99870400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:99862000-99868200	Weak transcription	Primary B cells from cord blood	blood
17	chr3:99862200-99863200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:99862200-99874200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:99862800-99870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links