Variant report

Variant	rs1779186
Chromosome Location	chr1:77667709-77667710
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10493600	0.86[MEX][hapmap]
rs1098121	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1098125	1.00[MEX][hapmap]
rs1098129	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1098130	1.00[MEX][hapmap]
rs1098132	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1098133	0.87[AFR][1000 genomes]
rs1103683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1253224	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1253226	0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs1266316	0.86[AFR][1000 genomes]
rs1270993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12723684	0.83[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs12744696	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12746974	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12760157	0.86[MEX][hapmap]
rs1419249	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs1502526	0.90[JPT][hapmap]
rs1502529	0.86[MEX][hapmap]
rs1502533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1615806	0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs17099885	0.90[JPT][hapmap]
rs17099982	0.89[JPT][hapmap]
rs17099983	0.90[JPT][hapmap]
rs17099986	0.90[JPT][hapmap]
rs17100001	0.90[JPT][hapmap]
rs17100002	0.89[JPT][hapmap]
rs17100005	0.90[JPT][hapmap]
rs17100021	0.90[JPT][hapmap]
rs17100026	0.90[JPT][hapmap]
rs1721127	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1721140	0.86[AFR][1000 genomes]
rs1721145	0.81[YRI][hapmap];0.88[AFR][1000 genomes]
rs1721151	0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs1779189	0.86[AFR][1000 genomes]
rs1779198	0.83[ASW][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes]
rs2653469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2689666	0.83[AFR][1000 genomes]
rs2689674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2689675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2689678	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2689679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2762882	0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[AFR][1000 genomes]
rs2799564	0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs35446093	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67263641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71658787	0.87[AFR][1000 genomes]
rs72681896	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs839808	0.81[YRI][hapmap];0.91[AFR][1000 genomes]
rs839810	0.81[YRI][hapmap];0.91[AFR][1000 genomes]
rs839814	0.91[AFR][1000 genomes]
rs839818	0.81[YRI][hapmap];0.91[AFR][1000 genomes]
rs839820	0.90[JPT][hapmap]
rs839821	0.89[JPT][hapmap]
rs839822	0.80[YRI][hapmap];0.90[AFR][1000 genomes]
rs839823	0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.87[AFR][1000 genomes]
rs839824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs839826	0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs839827	0.87[AFR][1000 genomes]
rs839830	0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs839831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs858447	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77626000-77684200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:77626800-77668000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:77626800-77674800	Weak transcription	Ovary	ovary
4	chr1:77626800-77676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:77643400-77669600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:77643600-77672600	Weak transcription	Fetal Lung	lung
7	chr1:77643800-77674400	Weak transcription	Psoas Muscle	Psoas
8	chr1:77648400-77684000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:77649000-77679800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:77649200-77672400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:77650800-77668800	Weak transcription	Adipose Nuclei	Adipose
12	chr1:77650800-77672000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:77650800-77684200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:77651200-77668000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:77652600-77683400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:77653200-77670800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:77653400-77667800	Weak transcription	NHDF-Ad	bronchial
18	chr1:77654000-77669600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:77655000-77673400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:77655200-77673000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:77655200-77680400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:77655200-77684000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:77655400-77669000	Weak transcription	Fetal Intestine Small	intestine
24	chr1:77655600-77683200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:77655800-77670800	Weak transcription	Dnd41	blood
26	chr1:77656400-77669800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr1:77656600-77669600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:77657400-77680000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:77657400-77681200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:77658400-77669600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:77659200-77671000	Weak transcription	Aorta	Aorta
32	chr1:77659200-77683200	Weak transcription	Brain Angular Gyrus	brain
33	chr1:77660800-77669400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:77660800-77672200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:77661000-77669600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:77661000-77669800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:77661000-77671000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:77661200-77669600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:77661200-77676400	Weak transcription	Left Ventricle	heart
40	chr1:77662000-77669400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:77662000-77670800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:77662200-77671800	Weak transcription	Primary T cells from cord blood	blood
43	chr1:77664200-77669600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:77666000-77679800	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:77666800-77683400	Weak transcription	NHLF	lung

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