Variant report

Variant	rs1342152
Chromosome Location	chr1:212461169-212461170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212317380..212319977-chr1:212460933..212463499,2	K562	blood:
2	chr1:212459558..212461570-chr1:212482463..212485190,2	K562	blood:
3	chr1:212459145..212461703-chr1:212522964..212525110,2	K562	blood:
4	chr1:212247974..212251489-chr1:212456327..212461743,5	MCF-7	breast:
5	chr1:212413271..212416807-chr1:212458908..212461742,4	K562	blood:
6	chr1:212270755..212277124-chr1:212457942..212461824,7	K562	blood:

Variant related genes	Relation type
ENSG00000264358	Chromatin interaction
ENSG00000252879	Chromatin interaction
ENSG00000225338	Chromatin interaction
ENSG00000143476	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1056985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863955	0.93[CEU][hapmap]
rs10863956	1.00[AFR][1000 genomes]
rs10863965	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs11119886	0.93[CEU][hapmap];1.00[AFR][1000 genomes]
rs11119891	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs11119893	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11119903	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119907	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119908	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119910	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119918	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11119932	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs11119934	0.93[CEU][hapmap];0.95[CHB][hapmap]
rs12118709	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12118732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12119779	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12124582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12128123	0.83[EUR][1000 genomes]
rs12128965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12129267	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12133582	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs12133636	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12134074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12134599	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12136095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12137798	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138533	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12140158	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12141427	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12143853	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12145170	0.81[ASN][1000 genomes]
rs12145377	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12145484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12146141	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12239580	1.00[CHB][hapmap]
rs12403586	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12561785	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12562618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1493601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17018777	0.93[CEU][hapmap]
rs17018847	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17018853	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2166155	1.00[CHB][hapmap]
rs2236598	0.99[ASN][1000 genomes]
rs2298115	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754142	0.83[CHB][hapmap]
rs3754144	0.95[CHB][hapmap]
rs3767867	1.00[CHB][hapmap]
rs3767868	0.95[CHB][hapmap]
rs3820513	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4951597	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs61260530	0.81[AMR][1000 genomes]
rs903119	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1342152	PPP2R5A	cis	Whole Blood	GTEx
rs1342152	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs1342152	PPP2R5A	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212457000-212461400	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:212457000-212461600	Active TSS	Colonic Mucosa	Colon
3	chr1:212457200-212461600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:212457200-212461600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:212457400-212461400	Active TSS	Fetal Intestine Large	intestine
6	chr1:212457400-212461800	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:212457400-212463400	Active TSS	Right Ventricle	heart
8	chr1:212457600-212461400	Active TSS	Left Ventricle	heart
9	chr1:212457600-212461600	Active TSS	NHDF-Ad	bronchial
10	chr1:212457600-212461800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:212457600-212461800	Active TSS	Esophagus	oesophagus
12	chr1:212457600-212462400	Active TSS	Aorta	Aorta
13	chr1:212457600-212462800	Active TSS	Psoas Muscle	Psoas
14	chr1:212457800-212461600	Active TSS	Lung	lung
15	chr1:212457800-212461600	Active TSS	GM12878-XiMat	blood
16	chr1:212457800-212461800	Active TSS	Gastric	stomach
17	chr1:212458000-212461400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:212458000-212461400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:212458000-212461400	Active TSS	Liver	Liver
20	chr1:212458000-212461400	Active TSS	Fetal Intestine Small	intestine
21	chr1:212458000-212461400	Active TSS	Ovary	ovary
22	chr1:212458000-212461400	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr1:212458000-212461600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:212458000-212461600	Active TSS	Rectal Smooth Muscle	rectum
25	chr1:212458000-212461600	Active TSS	Hela-S3	cervix
26	chr1:212458000-212461800	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:212458000-212463400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:212458200-212461400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:212458200-212461400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:212458200-212461400	Active TSS	Brain Hippocampus Middle	brain
31	chr1:212458200-212461400	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:212458200-212461600	Active TSS	NHLF	lung
33	chr1:212458200-212462000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:212458400-212461400	Active TSS	Primary T cells fromperipheralblood	blood
35	chr1:212458400-212461400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:212459800-212461200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:212459800-212461600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:212459800-212462800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:212459800-212463000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr1:212459800-212463000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr1:212460000-212461400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr1:212460000-212463800	Active TSS	Right Atrium	heart
43	chr1:212460200-212461400	Flanking Active TSS	HUVEC	blood vessel
44	chr1:212460200-212462800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr1:212460200-212462800	Flanking Active TSS	Dnd41	blood
46	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
47	chr1:212460400-212461200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr1:212460400-212461400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr1:212460400-212462600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:212460400-212463000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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