Variant report

Variant	rs1166709
Chromosome Location	chr1:78334255-78334256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001070	1.00[YRI][hapmap]
rs10437022	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs10873956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162390	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162400	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1166697	0.82[AMR][1000 genomes]
rs1166702	0.81[CHB][hapmap]
rs1166704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166705	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1166707	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11807240	0.81[CHB][hapmap]
rs12021502	1.00[CEU][hapmap]
rs12405212	0.81[CHB][hapmap]
rs12409561	0.81[CHB][hapmap]
rs12723748	0.80[AMR][1000 genomes]
rs1335481	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1539737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1555798	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs1626757	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17383213	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17387365	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2154138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274124	1.00[CEU][hapmap]
rs2274257	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs2296453	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs3767028	0.81[CHB][hapmap]
rs4949828	0.81[CHB][hapmap]
rs4949829	0.81[CHB][hapmap]
rs6424664	1.00[YRI][hapmap]
rs6656888	0.81[CHB][hapmap]
rs6659045	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667733	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677890	1.00[YRI][hapmap]
rs7417104	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs750720	0.81[CHB][hapmap]
rs7514007	1.00[YRI][hapmap]
rs7544892	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9324166	0.82[AMR][1000 genomes]
rs9659938	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv1004327	chr1:78212804-78352385	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1006600	chr1:78222312-78384009	Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv535011	chr1:78222312-78384009	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78282800-78353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:78298400-78340400	Weak transcription	Colonic Mucosa	Colon
3	chr1:78298600-78352400	Weak transcription	Right Ventricle	heart
4	chr1:78299400-78340200	Weak transcription	NHEK	skin
5	chr1:78299400-78341200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:78299600-78340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:78299600-78343000	Weak transcription	K562	blood
8	chr1:78299600-78353800	Weak transcription	Brain Substantia Nigra	brain
9	chr1:78300800-78342200	Weak transcription	Fetal Brain Male	brain
10	chr1:78301400-78353200	Weak transcription	HSMMtube	muscle
11	chr1:78301800-78342400	Weak transcription	NHLF	lung
12	chr1:78305800-78342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:78306000-78342600	Weak transcription	Brain Angular Gyrus	brain
14	chr1:78309200-78352400	Weak transcription	Aorta	Aorta
15	chr1:78312000-78353000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:78313000-78353200	Weak transcription	HUVEC	blood vessel
17	chr1:78313400-78343200	Weak transcription	Pancreas	Pancrea
18	chr1:78323800-78340600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:78324400-78334600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:78324400-78334600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:78324600-78353800	Weak transcription	Esophagus	oesophagus
22	chr1:78324800-78340200	Weak transcription	Hela-S3	cervix
23	chr1:78325000-78334600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr1:78325600-78334600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr1:78326000-78334400	Strong transcription	Primary T cells from cord blood	blood
26	chr1:78326400-78341600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:78327200-78353600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:78327400-78353800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:78327800-78334400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:78328400-78334600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:78328600-78334600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:78328600-78336400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:78328800-78334600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:78329000-78334600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:78329000-78334600	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:78329000-78340400	Weak transcription	A549	lung
37	chr1:78329200-78334600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:78329400-78340600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:78329600-78344400	Weak transcription	GM12878-XiMat	blood
40	chr1:78329800-78334400	Strong transcription	Fetal Intestine Small	intestine
41	chr1:78330000-78344400	Weak transcription	Small Intestine	intestine
42	chr1:78330200-78334400	Strong transcription	Fetal Intestine Large	intestine
43	chr1:78330400-78334400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:78330400-78334600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:78330800-78346600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:78331000-78334400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:78331000-78334400	Strong transcription	Adipose Nuclei	Adipose
48	chr1:78331400-78342600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:78331600-78334400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:78331600-78334400	Strong transcription	Left Ventricle	heart

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