Variant report

Variant	rs10465863
Chromosome Location	chr1:70778513-70778514
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11209599	1.00[CEU][hapmap]
rs11209600	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209603	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209608	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11209611	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11800138	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029977	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12030275	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs12031053	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12034101	0.91[AMR][1000 genomes]
rs12036256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12037272	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042565	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12565458	0.86[AMR][1000 genomes]
rs12565460	0.84[AMR][1000 genomes]
rs1327873	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs17131276	0.84[CEU][hapmap];0.84[AMR][1000 genomes]
rs17131285	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs1969953	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4560989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4650038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650041	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4650047	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs56211824	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58696538	0.85[AFR][1000 genomes]
rs58997663	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59821213	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60602940	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61122312	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61587863	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61678482	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6686181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72678630	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72678644	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72678645	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72678646	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72680732	0.84[AMR][1000 genomes]
rs7539544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs768433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014292	chr1:70689215-70799065	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	esv1792702	chr1:70755511-70818576	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv871430	chr1:70765659-70819912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10465863	SFRS11	Cis_1M	lymphoblastoid	RTeQTL
rs10465863	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70716800-70815800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:70717600-70780400	Weak transcription	Brain Substantia Nigra	brain
4	chr1:70717800-70788200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:70719200-70783800	Weak transcription	A549	lung
6	chr1:70734000-70786000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:70734400-70786000	Weak transcription	Psoas Muscle	Psoas
8	chr1:70734400-70813000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:70752800-70793400	Weak transcription	Gastric	stomach
10	chr1:70754200-70780400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:70757000-70799800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:70757400-70813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:70757800-70786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:70757800-70799400	Weak transcription	Brain Germinal Matrix	brain
15	chr1:70757800-70812400	Weak transcription	Fetal Brain Male	brain
16	chr1:70759400-70785400	Weak transcription	HMEC	breast
17	chr1:70760200-70799800	Weak transcription	Lung	lung
18	chr1:70760400-70802400	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:70760400-70813200	Weak transcription	Fetal Brain Female	brain
20	chr1:70760600-70783600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:70760600-70818200	Weak transcription	Aorta	Aorta
22	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
23	chr1:70761800-70785400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:70762000-70817600	Weak transcription	NHLF	lung
25	chr1:70762200-70818200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:70765400-70799200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:70765600-70818200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:70765800-70783800	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:70765800-70788200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:70765800-70799400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:70765800-70812200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:70766000-70780400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:70766200-70780600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:70767400-70789800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:70767600-70783600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:70767600-70784800	Weak transcription	Primary B cells from cord blood	blood
37	chr1:70767600-70785600	Weak transcription	NHDF-Ad	bronchial
38	chr1:70767600-70786600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:70767600-70788000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:70767600-70798600	Weak transcription	K562	blood
41	chr1:70767800-70785200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:70767800-70785200	Weak transcription	HUVEC	blood vessel
43	chr1:70767800-70785400	Weak transcription	NH-A	brain
44	chr1:70767800-70785600	Weak transcription	HSMM	muscle
45	chr1:70767800-70786600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:70767800-70789800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:70767800-70799200	Weak transcription	Placenta	Placenta
48	chr1:70767800-70819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:70768000-70785600	Weak transcription	Hela-S3	cervix
50	chr1:70768200-70784000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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