Variant report

Variant	rs12071212
Chromosome Location	chr1:78003764-78003765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1013399	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782654	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873949	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10873950	0.93[ASN][1000 genomes]
rs10873951	0.82[ASN][1000 genomes]
rs11162362	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162363	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11162364	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162365	0.90[ASN][1000 genomes]
rs11162369	0.83[ASN][1000 genomes]
rs11162372	0.81[ASN][1000 genomes]
rs12074409	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12095064	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12717767	0.90[ASN][1000 genomes]
rs12724560	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565850	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1565851	0.95[ASN][1000 genomes]
rs1565852	0.86[ASN][1000 genomes]
rs1962523	0.89[ASN][1000 genomes]
rs1976334	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029768	0.97[ASN][1000 genomes]
rs2133202	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2172727	0.96[ASN][1000 genomes]
rs2647486	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647487	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2803136	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2803168	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34773766	0.89[ASN][1000 genomes]
rs3509	0.93[ASN][1000 genomes]
rs3738079	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767033	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4245658	0.95[ASN][1000 genomes]
rs4589153	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4600093	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949657	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949658	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949659	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949807	0.95[ASN][1000 genomes]
rs4949808	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949809	0.95[ASN][1000 genomes]
rs4949811	0.92[ASN][1000 genomes]
rs4949813	0.91[ASN][1000 genomes]
rs4949816	0.86[ASN][1000 genomes]
rs6603952	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6603953	0.91[ASN][1000 genomes]
rs6603955	0.90[ASN][1000 genomes]
rs6667519	0.95[ASN][1000 genomes]
rs6667803	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675743	0.95[ASN][1000 genomes]
rs6692369	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695989	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6696083	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728741	0.91[ASN][1000 genomes]
rs7513619	0.81[ASN][1000 genomes]
rs7519476	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524147	0.94[ASN][1000 genomes]
rs7524866	0.95[ASN][1000 genomes]
rs7531286	0.91[ASN][1000 genomes]
rs7545544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551211	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551729	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962388	0.91[ASN][1000 genomes]
rs9787153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:77998200-78005000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:77999200-78004600	Enhancers	NH-A	brain
5	chr1:77999600-78003800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:77999600-78004000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:77999600-78009600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:77999800-78005200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:78000000-78003800	Genic enhancers	NHDF-Ad	bronchial
10	chr1:78000000-78004400	Weak transcription	Fetal Kidney	kidney
11	chr1:78000000-78005000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:78000000-78011600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:78000200-78004600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:78000200-78004600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:78000200-78004600	Weak transcription	Brain Substantia Nigra	brain
18	chr1:78000200-78005000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:78000200-78005000	Weak transcription	Brain Anterior Caudate	brain
20	chr1:78000800-78006800	Strong transcription	Primary T cells from cord blood	blood
21	chr1:78001000-78004800	Enhancers	Hela-S3	cervix
22	chr1:78001000-78004800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:78001000-78005000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:78001200-78004600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:78001400-78003800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:78001400-78004000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:78001400-78004800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:78001400-78006600	Enhancers	NHEK	skin
29	chr1:78001600-78005000	Enhancers	HSMM	muscle
30	chr1:78001600-78005800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:78001600-78006200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:78001600-78006600	Enhancers	HMEC	breast
33	chr1:78001800-78006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:78002000-78003800	Enhancers	HUVEC	blood vessel
35	chr1:78002000-78004800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:78002200-78004400	Enhancers	A549	lung
37	chr1:78002200-78004600	Enhancers	HSMMtube	muscle
38	chr1:78002200-78004600	Enhancers	Osteobl	bone
39	chr1:78002200-78005200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:78002400-78004800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:78002400-78004800	Enhancers	NHLF	lung
42	chr1:78002800-78004000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:78003000-78004400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:78003000-78005000	Weak transcription	Gastric	stomach
45	chr1:78003200-78004800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:78003200-78004800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:78003200-78004800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:78003400-78004400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:78003400-78004400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:78003400-78004600	Weak transcription	Brain Cingulate Gyrus	brain

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