Variant report

Variant	rs6798114
Chromosome Location	chr3:99892825-99892826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10222474	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487143	1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12488245	0.88[CEU][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs12629505	0.84[ASN][1000 genomes]
rs1387647	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs2130369	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316263	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4928151	0.84[CEU][hapmap]
rs4928153	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs4928237	0.84[CEU][hapmap]
rs6440967	0.84[CEU][hapmap]
rs6767441	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	0.84[CEU][hapmap]
rs6806323	0.84[CEU][hapmap]
rs720688	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7619080	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7629487	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636776	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7649349	0.84[CEU][hapmap]
rs766778	0.84[CEU][hapmap]
rs902159	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs923472	0.84[CEU][hapmap]
rs9289981	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811920	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837131	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9849632	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9865713	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	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	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6798114	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99865000-99894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:99865600-99898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:99868000-99897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:99869000-99895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:99869000-99897800	Weak transcription	Pancreas	Pancrea
6	chr3:99870400-99898600	Weak transcription	Esophagus	oesophagus
7	chr3:99871400-99899400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:99874400-99894400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:99874400-99897000	Weak transcription	K562	blood
10	chr3:99874600-99897400	Weak transcription	A549	lung
11	chr3:99874800-99895200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:99874800-99897200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:99874800-99897200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:99874800-99897200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:99874800-99898200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:99874800-99898400	Weak transcription	HepG2	liver
17	chr3:99875000-99897400	Weak transcription	GM12878-XiMat	blood
18	chr3:99876600-99894800	Weak transcription	Right Atrium	heart
19	chr3:99876600-99897200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:99876600-99897400	Weak transcription	Fetal Intestine Small	intestine
21	chr3:99877600-99904600	Weak transcription	Right Ventricle	heart
22	chr3:99878000-99897200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:99878400-99897200	Weak transcription	Fetal Thymus	thymus
24	chr3:99878400-99898200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:99879200-99894000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:99879200-99897400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:99879200-99897400	Weak transcription	NHEK	skin
28	chr3:99879200-99898600	Weak transcription	Hela-S3	cervix
29	chr3:99879400-99896800	Weak transcription	Fetal Intestine Large	intestine
30	chr3:99880000-99894400	Weak transcription	HSMM	muscle
31	chr3:99880200-99897400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:99880200-99898600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:99880600-99894600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:99881600-99894800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:99883000-99898400	Weak transcription	HSMMtube	muscle
36	chr3:99883200-99894400	Weak transcription	Ovary	ovary
37	chr3:99883400-99898400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:99883400-99898600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:99883600-99897400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:99883800-99894200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:99883800-99898800	Weak transcription	NHDF-Ad	bronchial
42	chr3:99884000-99897400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:99885200-99897200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:99885400-99896200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:99885600-99897200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:99885600-99897600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:99885800-99897600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:99886600-99897200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:99886600-99897400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:99887000-99897200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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