Variant report

Variant	rs9729146
Chromosome Location	chr1:78388105-78388106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1039863	0.93[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10735751	0.93[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10873961	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10873962	0.87[ASN][1000 genomes]
rs10873963	0.93[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs11162401	0.93[ASN][1000 genomes]
rs1166696	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1166699	1.00[ASN][1000 genomes]
rs1166700	0.85[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805942	0.93[ASN][1000 genomes]
rs11806130	0.96[ASN][1000 genomes]
rs11811805	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1510244	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17101101	0.93[ASN][1000 genomes]
rs1749911	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1749913	1.00[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][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]
rs1780044	0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs1780045	0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1780047	0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs1780048	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1780052	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296452	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296454	0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs3736909	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3767024	0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs3767025	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3790586	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4083559	0.97[ASN][1000 genomes]
rs4107671	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4483454	1.00[ASN][1000 genomes]
rs4543852	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4631748	0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs6424648	0.93[ASW][hapmap];0.85[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424653	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6675105	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6680447	0.92[ASN][1000 genomes]
rs6699513	0.87[ASN][1000 genomes]
rs6702465	0.85[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72685363	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72685364	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72685368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7520255	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7523874	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7524504	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547599	0.81[JPT][hapmap]
rs9661687	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9662129	0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78356200-78408600	Weak transcription	HMEC	breast
2	chr1:78356400-78396000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:78367000-78407000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:78371600-78413000	Weak transcription	Psoas Muscle	Psoas
5	chr1:78372800-78418600	Weak transcription	Pancreas	Pancrea
6	chr1:78381400-78390600	Strong transcription	Osteobl	bone
7	chr1:78381600-78395200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:78381800-78390600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:78381800-78390800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:78382200-78390800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:78382200-78407400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:78382200-78408000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:78382400-78394000	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:78382400-78405600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:78382800-78395800	Weak transcription	NHDF-Ad	bronchial
16	chr1:78383000-78400000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:78383200-78389800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:78383600-78391000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:78383600-78418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:78383800-78389600	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:78383800-78404000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:78384000-78388200	Strong transcription	Aorta	Aorta
23	chr1:78384000-78395400	Weak transcription	Fetal Heart	heart
24	chr1:78384200-78392200	Weak transcription	Adipose Nuclei	Adipose
25	chr1:78384400-78391800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:78384400-78395400	Weak transcription	Right Ventricle	heart
27	chr1:78384600-78389800	Weak transcription	NHLF	lung
28	chr1:78384600-78391800	Weak transcription	HUVEC	blood vessel
29	chr1:78384600-78396400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:78384600-78406000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:78385000-78391800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:78385200-78389800	Weak transcription	Fetal Lung	lung
33	chr1:78385200-78390800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:78385200-78400000	Weak transcription	Fetal Intestine Large	intestine
35	chr1:78385600-78396400	Weak transcription	Ovary	ovary
36	chr1:78386200-78392400	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:78386600-78388800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:78387000-78389000	Weak transcription	NH-A	brain
39	chr1:78387000-78389400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:78387000-78390600	Strong transcription	Fetal Stomach	stomach
41	chr1:78387000-78391600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:78387600-78388600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:78387600-78392200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:78387600-78395000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:78387600-78395200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:78387600-78399400	Weak transcription	Fetal Intestine Small	intestine
47	chr1:78387800-78388800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:78387800-78391800	Weak transcription	Left Ventricle	heart
49	chr1:78387800-78392400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:78387800-78412600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links