Variant report

Variant	rs13074817
Chromosome Location	chr3:111467155-111467156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD96-3	chr3:111466665-111467424	NONHSAT091151

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10212300	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10470303	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10934106	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934107	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11711582	0.95[GIH][hapmap]
rs12490166	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490595	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496925	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496971	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12497012	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13069980	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079085	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2137595	0.89[GIH][hapmap]
rs4284954	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4413291	0.89[GIH][hapmap]
rs4431081	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4682299	0.95[GIH][hapmap]
rs4682305	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs62273780	0.94[ASN][1000 genomes]
rs6438003	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6438008	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438009	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764720	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768713	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777540	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6784441	0.81[CHD][hapmap]
rs6784753	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6786386	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6786612	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6788543	0.98[GIH][hapmap]
rs6790072	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6790079	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792493	0.84[ASN][1000 genomes]
rs6796087	0.98[GIH][hapmap]
rs6802995	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7427201	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7609653	0.99[ASN][1000 genomes]
rs7614443	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818574	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9823974	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9825915	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9834030	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838371	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863403	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9868171	0.94[ASN][1000 genomes]
rs9868909	0.98[GIH][hapmap]
rs9870823	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111458600-111467200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:111462600-111468000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:111462600-111468000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:111463000-111469600	Weak transcription	Adipose Nuclei	Adipose
5	chr3:111463800-111468200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:111465000-111469200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:111465200-111468000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:111465200-111468200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:111465200-111468400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:111465400-111469600	Weak transcription	A549	lung
11	chr3:111465400-111470400	Weak transcription	Hela-S3	cervix
12	chr3:111466000-111467400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:111466200-111467200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:111466200-111471400	Enhancers	NHEK	skin
15	chr3:111466400-111467200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:111466400-111467200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:111466400-111467400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:111466400-111467400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:111466400-111467400	Enhancers	Gastric	stomach
20	chr3:111466400-111467400	Enhancers	HMEC	breast
21	chr3:111466400-111467400	Enhancers	NH-A	brain
22	chr3:111466400-111467600	Enhancers	HepG2	liver
23	chr3:111466400-111468200	Enhancers	HUVEC	blood vessel
24	chr3:111466400-111469400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:111466400-111469600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:111466400-111471200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:111466400-111471400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:111466600-111467200	Enhancers	Osteobl	bone
29	chr3:111466600-111467400	Enhancers	Stomach Mucosa	stomach
30	chr3:111466600-111471000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:111466800-111467200	Enhancers	Small Intestine	intestine
32	chr3:111466800-111467400	Enhancers	Liver	Liver
33	chr3:111466800-111467800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:111466800-111471200	Enhancers	HSMM	muscle
35	chr3:111467000-111467200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:111467000-111467200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:111467000-111467200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr3:111467000-111467200	Enhancers	NHDF-Ad	bronchial
39	chr3:111467000-111467400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr3:111467000-111467400	Enhancers	Rectal Smooth Muscle	rectum
41	chr3:111467000-111467400	Enhancers	Right Ventricle	heart
42	chr3:111467000-111467800	Enhancers	Fetal Muscle Leg	muscle
43	chr3:111467000-111469000	Enhancers	Fetal Kidney	kidney

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