Variant report

Variant	rs2542573
Chromosome Location	chr2:54046646-54046647
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10490468	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11897282	0.92[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs11901698	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs1232	0.92[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs13408029	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs17045176	0.93[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs17045199	0.87[CEU][hapmap]
rs17045203	0.92[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs17520505	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17521008	0.84[ASN][1000 genomes]
rs2287340	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs2302797	0.92[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs2542572	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2542578	0.87[ASN][1000 genomes]
rs2542580	0.92[ASN][1000 genomes]
rs2542582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2542583	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2542589	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542590	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542591	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542592	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2543629	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs2692512	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692513	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692516	0.83[CEU][hapmap]
rs2692519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2692521	0.91[ASN][1000 genomes]
rs2692522	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692523	0.87[ASN][1000 genomes]
rs2692530	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2692533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692534	0.92[CEU][hapmap]
rs2909262	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2949813	0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2949814	0.87[ASN][1000 genomes]
rs35772199	0.84[ASN][1000 genomes]
rs3770394	0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs3770395	0.85[ASN][1000 genomes]
rs3770397	0.88[ASN][1000 genomes]
rs3770399	0.85[ASN][1000 genomes]
rs3770411	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs4116709	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs62137573	0.84[ASN][1000 genomes]
rs62137602	0.88[ASN][1000 genomes]
rs62137606	0.85[ASN][1000 genomes]
rs62137610	0.82[ASN][1000 genomes]
rs62137611	0.82[ASN][1000 genomes]
rs62137612	0.82[ASN][1000 genomes]
rs6730006	0.85[ASN][1000 genomes]
rs719127	0.93[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs72901256	0.87[ASN][1000 genomes]
rs7600817	0.85[ASN][1000 genomes]
rs805316	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs805334	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs805338	0.93[CHB][hapmap]
rs805368	0.88[ASN][1000 genomes]
rs805383	0.89[ASN][1000 genomes]
rs805385	0.89[ASN][1000 genomes]
rs805398	0.85[ASN][1000 genomes]
rs805413	0.80[ASN][1000 genomes]
rs805435	0.89[ASN][1000 genomes]
rs805437	0.91[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs805446	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs805447	0.93[CHB][hapmap]
rs805449	0.92[CHB][hapmap]

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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2542573	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
2	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:54020600-54048600	Strong transcription	Osteobl	bone
8	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
13	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:54021400-54047000	Strong transcription	Fetal Thymus	thymus
16	chr2:54021800-54047600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:54022000-54047000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:54022000-54047000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:54022000-54047200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:54022000-54047600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:54022200-54047200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
24	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:54030200-54047200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
27	chr2:54031400-54047200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:54032800-54046800	Strong transcription	Primary B cells from cord blood	blood
29	chr2:54033000-54047200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:54034400-54047200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:54034600-54047200	Strong transcription	HSMM	muscle
32	chr2:54035800-54052800	Weak transcription	Brain Substantia Nigra	brain
33	chr2:54037200-54047200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:54038800-54053000	Weak transcription	Fetal Brain Male	brain
35	chr2:54039600-54047000	Strong transcription	A549	lung
36	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
37	chr2:54040600-54047200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:54040600-54053000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:54040800-54048000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:54040800-54053000	Weak transcription	Brain Angular Gyrus	brain
41	chr2:54040800-54053000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:54041400-54049200	Weak transcription	K562	blood
43	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
44	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:54042200-54046800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr2:54042200-54047600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:54042400-54046800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:54042400-54047200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr2:54042400-54047200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:54042400-54048200	Strong transcription	Stomach Smooth Muscle	stomach

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