Variant report

Variant	rs482291
Chromosome Location	chr1:70878852-70878853
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70876526..70879847-chr1:71510519..71513789,3	K562	blood:
2	chr1:70688440..70690850-chr1:70877083..70879333,2	K562	blood:
3	chr1:70878824..70881393-chr1:70902317..70904279,2	MCF-7	breast:
4	chr1:70877825..70880614-chr1:70884736..70887414,2	K562	blood:
5	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
6	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:

Variant related genes	Relation type
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction
ENSG00000050628	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493473	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10518334	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11209612	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11209613	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12116830	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12118663	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12126226	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12137720	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12725762	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12730494	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12737233	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12741805	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12741941	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12751638	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35481139	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs490574	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	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs513263	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs542842	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs543860	0.88[EUR][1000 genomes]
rs561926	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs618531	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs664051	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71500608	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71651454	0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs482291	HHLA3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70875800-70879000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr1:70875800-70879000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:70875800-70879000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:70875800-70879800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:70875800-70880000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:70876000-70879000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:70876000-70879000	Active TSS	K562	blood
8	chr1:70876200-70879000	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr1:70876200-70879600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:70876400-70880200	Active TSS	Liver	Liver
11	chr1:70877400-70898600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:70877400-70900600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:70877400-70900600	Weak transcription	Lung	lung
14	chr1:70877400-70901800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:70877400-70903400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:70877400-70906400	Weak transcription	Small Intestine	intestine
17	chr1:70877400-70906600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:70877600-70891000	Weak transcription	Left Ventricle	heart
19	chr1:70877600-70892000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:70877800-70882000	Weak transcription	Fetal Stomach	stomach
21	chr1:70877800-70907800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:70878000-70879000	Active TSS	HepG2	liver
23	chr1:70878000-70899000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:70878000-70903400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:70878000-70908200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:70878200-70879000	Flanking Active TSS	GM12878-XiMat	blood
27	chr1:70878200-70882400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:70878200-70882600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:70878200-70885000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:70878200-70891000	Weak transcription	Aorta	Aorta
31	chr1:70878200-70899200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:70878200-70907000	Weak transcription	Psoas Muscle	Psoas
33	chr1:70878200-70909600	Weak transcription	Gastric	stomach
34	chr1:70878400-70879000	Active TSS	Brain Angular Gyrus	brain
35	chr1:70878400-70879800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:70878400-70879800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:70878400-70879800	Weak transcription	Pancreas	Pancrea
38	chr1:70878400-70883600	Weak transcription	Fetal Intestine Large	intestine
39	chr1:70878400-70885600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:70878400-70891000	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:70878400-70895400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:70878400-70896600	Weak transcription	Adipose Nuclei	Adipose
43	chr1:70878400-70897600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:70878400-70897600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:70878400-70897800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:70878400-70899200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr1:70878400-70901800	Weak transcription	Colonic Mucosa	Colon
48	chr1:70878400-70907000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:70878600-70879000	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:70878600-70879000	Active TSS	NHEK	skin

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