Variant report

Variant	rs490574
Chromosome Location	chr1:70877495-70877496
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70876951..70877911-chr1:155196685..155197597,2	Hela-S3	cervix:
2	chr1:70876526..70879847-chr1:71510519..71513789,3	K562	blood:
3	chr1:70688440..70690850-chr1:70877083..70879333,2	K562	blood:
4	chr1:70877206..70877981-chr10:52383708..52384377,2	Hela-S3	cervix:
5	chr1:70876874..70877654-chr11:62608483..62609471,3	Hela-S3	cervix:
6	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
7	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
8	chr1:70779446..70781152-chr1:70876074..70878497,2	MCF-7	breast:
9	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197568	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000118454	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000050628	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10493473	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10518334	1.00[JPT][hapmap]
rs11209612	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11209613	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12116830	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12118663	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12126226	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12137720	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12725762	1.00[JPT][hapmap]
rs12730494	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12737233	1.00[JPT][hapmap]
rs12741805	1.00[JPT][hapmap]
rs12741941	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12751638	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35481139	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482291	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508310	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs513263	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs542842	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs543860	0.88[EUR][1000 genomes]
rs561926	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs618531	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs664051	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71500608	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71651454	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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	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
2	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
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs490574	HHLA3	cis	Esophagus Muscularis	GTEx
rs490574	HHLA3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70875600-70878000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:70875800-70877600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:70875800-70877800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:70875800-70878800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:70875800-70878800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:70875800-70879000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:70875800-70879000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:70875800-70879000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:70875800-70879800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:70875800-70880000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:70876000-70877600	Active TSS	Brain Germinal Matrix	brain
12	chr1:70876000-70877600	Active TSS	Fetal Kidney	kidney
13	chr1:70876000-70877600	Active TSS	Fetal Stomach	stomach
14	chr1:70876000-70877600	Active TSS	Left Ventricle	heart
15	chr1:70876000-70877800	Active TSS	Fetal Brain Male	brain
16	chr1:70876000-70877800	Active TSS	Stomach Mucosa	stomach
17	chr1:70876000-70878000	Bivalent/Poised TSS	HepG2	liver
18	chr1:70876000-70878200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:70876000-70878200	Active TSS	Aorta	Aorta
22	chr1:70876000-70878200	Active TSS	Colonic Mucosa	Colon
23	chr1:70876000-70878200	Active TSS	Psoas Muscle	Psoas
24	chr1:70876000-70878200	Active TSS	GM12878-XiMat	blood
25	chr1:70876000-70878400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr1:70876000-70878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:70876000-70878400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:70876000-70878400	Active TSS	Fetal Intestine Large	intestine
29	chr1:70876000-70878600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:70876000-70878600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:70876000-70878600	Active TSS	Ovary	ovary
32	chr1:70876000-70878600	Active TSS	Right Atrium	heart
33	chr1:70876000-70878600	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr1:70876000-70878800	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:70876000-70878800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:70876000-70878800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:70876000-70878800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:70876000-70878800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:70876000-70878800	Active TSS	Brain Substantia Nigra	brain
40	chr1:70876000-70878800	Active TSS	Right Ventricle	heart
41	chr1:70876000-70879000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr1:70876000-70879000	Active TSS	K562	blood
43	chr1:70876200-70877600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:70876200-70877600	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr1:70876200-70877600	Active TSS	Brain Anterior Caudate	brain
46	chr1:70876200-70877600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr1:70876200-70877600	Active TSS	NHDF-Ad	bronchial
48	chr1:70876200-70877800	Active TSS	Brain Hippocampus Middle	brain
49	chr1:70876200-70877800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:70876200-70877800	Active TSS	Fetal Heart	heart

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