Variant report

Variant	rs2130369
Chromosome Location	chr3:99873317-99873318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10222474	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12487143	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12488245	0.92[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12629505	0.83[ASN][1000 genomes]
rs13059754	0.88[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs1387647	0.88[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes]
rs2316263	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs4928150	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs4928151	0.88[CEU][hapmap]
rs4928153	0.88[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs4928237	0.88[CEU][hapmap]
rs6440967	0.88[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6767441	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]
rs6798114	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]
rs6802817	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6806323	0.88[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs720688	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619080	0.85[ASN][1000 genomes]
rs7629487	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7636776	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7649349	0.88[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs766778	0.88[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs902159	0.88[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs923472	0.88[CEU][hapmap]
rs9289981	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9811920	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814549	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837131	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849632	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865713	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2130369	C3orf26	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99856000-99877800	Weak transcription	Ovary	ovary
2	chr3:99858600-99877200	Weak transcription	HSMM	muscle
3	chr3:99860200-99874000	Weak transcription	A549	lung
4	chr3:99862200-99874200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:99863400-99873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:99863400-99874000	Weak transcription	NHEK	skin
7	chr3:99863600-99874000	Weak transcription	GM12878-XiMat	blood
8	chr3:99863800-99873600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:99863800-99874000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:99864000-99873400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:99864400-99886600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:99864600-99873600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:99865000-99873400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:99865000-99894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:99865400-99873800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:99865600-99898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:99866000-99874000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:99866400-99874200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:99867200-99874000	Weak transcription	K562	blood
20	chr3:99867400-99874000	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:99867600-99874000	Weak transcription	Dnd41	blood
22	chr3:99868000-99897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:99868400-99874000	Weak transcription	HepG2	liver
24	chr3:99868800-99873600	Weak transcription	Primary B cells from cord blood	blood
25	chr3:99869000-99873400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:99869000-99873600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:99869000-99873600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:99869000-99874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:99869000-99874800	Weak transcription	Thymus	Thymus
30	chr3:99869000-99876400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:99869000-99895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:99869000-99897800	Weak transcription	Pancreas	Pancrea
33	chr3:99869400-99874000	Weak transcription	Fetal Lung	lung
34	chr3:99869800-99874200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:99870200-99873600	Weak transcription	NHDF-Ad	bronchial
36	chr3:99870200-99873800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:99870400-99874000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:99870400-99874000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:99870400-99874200	Weak transcription	Osteobl	bone
40	chr3:99870400-99898600	Weak transcription	Esophagus	oesophagus
41	chr3:99870600-99876400	Weak transcription	Left Ventricle	heart
42	chr3:99870800-99873400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:99870800-99873600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:99871000-99874000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:99871000-99874000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:99871000-99874000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:99871000-99874000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:99871200-99873400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:99871200-99873600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:99871200-99874000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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