Variant report

Variant	rs1052620
Chromosome Location	chr3:136574521-136574522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136569165..136571514-chr3:136573850..136577535,3	K562	blood:
2	chr3:136573010..136575502-chr3:136579664..136581454,2	MCF-7	breast:
3	chr3:136573273..136574958-chr3:136579585..136582154,2	K562	blood:
4	chr3:136570853..136574850-chr3:136578134..136583503,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239213	Chromatin interaction
ENSG00000158092	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs13062352	1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13080786	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099657	0.87[AFR][1000 genomes]
rs13100192	1.00[ASN][1000 genomes]
rs13314357	0.93[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs13433683	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433688	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs13434116	1.00[ASN][1000 genomes]
rs17365792	1.00[ASN][1000 genomes]
rs1872239	1.00[ASN][1000 genomes]
rs2176269	1.00[ASN][1000 genomes]
rs28370972	1.00[ASN][1000 genomes]
rs28390205	1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28489326	1.00[ASN][1000 genomes]
rs28750366	1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34564818	1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs34804893	1.00[ASN][1000 genomes]
rs35096613	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35100027	1.00[ASN][1000 genomes]
rs35198484	1.00[ASN][1000 genomes]
rs35210994	1.00[ASN][1000 genomes]
rs35422852	1.00[ASN][1000 genomes]
rs35428413	1.00[ASN][1000 genomes]
rs35880395	1.00[ASN][1000 genomes]
rs36109616	1.00[ASN][1000 genomes]
rs4038586	1.00[ASN][1000 genomes]
rs4470449	1.00[ASN][1000 genomes]
rs66509730	1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	1.00[ASN][1000 genomes]
rs6767889	1.00[ASN][1000 genomes]
rs71336069	1.00[ASN][1000 genomes]
rs71336080	1.00[ASN][1000 genomes]
rs73230043	1.00[ASN][1000 genomes]
rs73230099	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231903	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289513	0.93[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813376	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819856	1.00[ASN][1000 genomes]
rs9820717	1.00[ASN][1000 genomes]
rs9828976	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838884	1.00[ASW][hapmap];0.93[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840500	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845862	0.93[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9847427	1.00[ASN][1000 genomes]
rs9850364	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857833	1.00[ASN][1000 genomes]
rs9858560	1.00[ASN][1000 genomes]
rs9860879	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865995	1.00[ASN][1000 genomes]
rs9867325	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871184	1.00[ASN][1000 genomes]
rs9873536	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875770	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877089	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9879531	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881831	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877530	chr3:136514310-136604697	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
2	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1052620	PPP2R3A	cis	parietal	SCAN
rs1052620	PPP2R3A	cis	cerebellum	SCAN
rs1052620	ERICH1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136552600-136579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:136554800-136578400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:136554800-136579400	Weak transcription	Fetal Lung	lung
4	chr3:136555400-136579200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:136555600-136577800	Weak transcription	Lung	lung
6	chr3:136555600-136579200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:136555600-136580000	Weak transcription	Esophagus	oesophagus
8	chr3:136558200-136575600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:136558200-136579200	Weak transcription	NHDF-Ad	bronchial
10	chr3:136558400-136579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:136558400-136579400	Weak transcription	Fetal Intestine Large	intestine
12	chr3:136558400-136579600	Weak transcription	NHEK	skin
13	chr3:136558600-136575600	Weak transcription	Aorta	Aorta
14	chr3:136558600-136578000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:136558600-136578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:136558600-136578800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:136558600-136579200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:136558600-136579200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:136558600-136579600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:136558600-136579600	Weak transcription	Liver	Liver
21	chr3:136558600-136579600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:136558600-136579600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:136558600-136579800	Weak transcription	HSMM	muscle
24	chr3:136558800-136578600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:136558800-136578800	Weak transcription	HMEC	breast
26	chr3:136558800-136579000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:136558800-136579200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:136558800-136579400	Weak transcription	Pancreas	Pancrea
29	chr3:136559000-136575400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:136559000-136579400	Weak transcription	Brain Angular Gyrus	brain
31	chr3:136559000-136579600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:136559000-136580000	Weak transcription	Left Ventricle	heart
33	chr3:136559200-136575800	Weak transcription	Right Atrium	heart
34	chr3:136559200-136579400	Weak transcription	Right Ventricle	heart
35	chr3:136559200-136579800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:136559400-136575000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:136559400-136575000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:136559600-136579400	Weak transcription	Placenta	Placenta
39	chr3:136559800-136579400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:136560200-136575600	Weak transcription	K562	blood
41	chr3:136560200-136579200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:136561200-136579800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:136561400-136579400	Weak transcription	Fetal Kidney	kidney
44	chr3:136561800-136576600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:136561800-136579400	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:136561800-136579400	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:136563000-136579000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:136563000-136579200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:136565200-136579200	Weak transcription	Fetal Intestine Small	intestine
50	chr3:136565400-136578200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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