Variant report

Variant	rs1142851
Chromosome Location	chr4:57369630-57369631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10212643	0.83[EUR][1000 genomes]
rs1140982	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934479	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934636	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11940993	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12640212	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12643989	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643996	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644498	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649799	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650288	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1579019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086759	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086773	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086801	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086830	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086838	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086868	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086898	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086919	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17086922	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271924	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34398021	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34419325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733326	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796539	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796540	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796549	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796550	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4076103	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55778537	0.82[ASN][1000 genomes]
rs55903333	0.82[ASN][1000 genomes]
rs55909588	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56129706	0.82[ASN][1000 genomes]
rs56296497	0.82[ASN][1000 genomes]
rs56362514	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57245446	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58654038	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59153415	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59686671	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59764923	0.80[ASN][1000 genomes]
rs59828502	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6830145	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831869	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7437839	0.85[EUR][1000 genomes]
rs7658340	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7688482	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1142851	SRP72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
2	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57335600-57370200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:57335800-57370200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:57335800-57370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:57336000-57369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:57336000-57370000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:57336000-57370000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:57336000-57370200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:57336000-57371000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:57336200-57370000	Strong transcription	Placenta	Placenta
12	chr4:57336200-57370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:57336400-57370200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:57342000-57370200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr4:57342400-57370800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:57342400-57371400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:57346000-57371400	Weak transcription	Pancreas	Pancrea
18	chr4:57352000-57371400	Weak transcription	Gastric	stomach
19	chr4:57352000-57371400	Weak transcription	Spleen	Spleen
20	chr4:57353800-57371400	Weak transcription	Fetal Brain Male	brain
21	chr4:57354600-57371400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:57355400-57369800	Weak transcription	Psoas Muscle	Psoas
23	chr4:57356600-57371400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:57357400-57371400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:57357400-57371800	Weak transcription	Small Intestine	intestine
26	chr4:57357600-57371400	Weak transcription	Brain Substantia Nigra	brain
27	chr4:57357800-57371200	Weak transcription	Colonic Mucosa	Colon
28	chr4:57359200-57371200	Weak transcription	Hela-S3	cervix
29	chr4:57360400-57371200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:57361200-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:57362400-57371400	Weak transcription	Aorta	Aorta
32	chr4:57362400-57371400	Weak transcription	Esophagus	oesophagus
33	chr4:57362400-57371400	Weak transcription	Right Ventricle	heart
34	chr4:57362600-57371400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:57362600-57371400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr4:57362800-57371400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:57363000-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:57363000-57371400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr4:57363200-57371200	Weak transcription	Fetal Stomach	stomach
40	chr4:57363200-57371400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:57363200-57371400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:57363200-57371400	Weak transcription	Fetal Lung	lung
43	chr4:57363200-57371400	Weak transcription	Ovary	ovary
44	chr4:57363200-57371400	Weak transcription	NHLF	lung
45	chr4:57363200-57371600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:57363200-57371600	Weak transcription	Lung	lung
47	chr4:57363800-57371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr4:57363800-57371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:57364000-57371200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:57364000-57371400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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