Variant report

Variant	rs58997663
Chromosome Location	chr1:70773564-70773565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70761212..70763376-chr1:70772596..70774368,2	K562	blood:
2	chr1:70771700..70774695-chr1:70774871..70777365,2	MCF-7	breast:
3	chr1:70690194..70693110-chr1:70772753..70775116,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10465863	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11209600	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209602	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209603	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11209608	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11209611	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11800138	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12028257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12029977	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12030275	0.86[AMR][1000 genomes]
rs12031053	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12034101	0.91[AMR][1000 genomes]
rs12036256	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12037272	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12042565	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12565458	0.86[AMR][1000 genomes]
rs12565460	0.84[AMR][1000 genomes]
rs1327873	0.86[AMR][1000 genomes]
rs17131276	0.84[AMR][1000 genomes]
rs17131285	0.84[AMR][1000 genomes]
rs1969953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4560989	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4650038	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4650041	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4650047	0.86[AMR][1000 genomes]
rs56211824	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59821213	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60602940	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61122312	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61587863	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61678482	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6686181	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72678630	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72678644	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72678645	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72678646	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72680732	0.84[AMR][1000 genomes]
rs7539544	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs768433	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs998523	0.91[AMR][1000 genomes];0.94[EUR][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
rs58997663	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs58997663	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70716000-70775600	Weak transcription	Spleen	Spleen
3	chr1:70716200-70775200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:70716800-70815800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:70717600-70780400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:70717800-70788200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:70719200-70783800	Weak transcription	A549	lung
8	chr1:70734000-70786000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:70734400-70786000	Weak transcription	Psoas Muscle	Psoas
10	chr1:70734400-70813000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:70752800-70793400	Weak transcription	Gastric	stomach
12	chr1:70754200-70780400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:70754600-70775400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:70755800-70775400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:70757000-70799800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:70757400-70813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:70757800-70786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:70757800-70799400	Weak transcription	Brain Germinal Matrix	brain
19	chr1:70757800-70812400	Weak transcription	Fetal Brain Male	brain
20	chr1:70759400-70785400	Weak transcription	HMEC	breast
21	chr1:70760200-70799800	Weak transcription	Lung	lung
22	chr1:70760400-70802400	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:70760400-70813200	Weak transcription	Fetal Brain Female	brain
24	chr1:70760600-70776400	Weak transcription	Left Ventricle	heart
25	chr1:70760600-70783600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:70760600-70818200	Weak transcription	Aorta	Aorta
27	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
28	chr1:70761800-70785400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:70762000-70817600	Weak transcription	NHLF	lung
30	chr1:70762200-70818200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:70763600-70775000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:70765400-70799200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:70765600-70818200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:70765800-70783800	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:70765800-70788200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:70765800-70799400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:70765800-70812200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:70766000-70774800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:70766000-70780400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:70766200-70773600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:70766200-70780600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:70766600-70775000	Weak transcription	Brain Anterior Caudate	brain
43	chr1:70767200-70777400	Weak transcription	Osteobl	bone
44	chr1:70767400-70777400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:70767400-70789800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:70767600-70775800	Weak transcription	Dnd41	blood
47	chr1:70767600-70777000	Weak transcription	NHEK	skin
48	chr1:70767600-70777600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:70767600-70783600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:70767600-70784800	Weak transcription	Primary B cells from cord blood	blood

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