Variant report

Variant	rs2542571
Chromosome Location	chr2:54041983-54041984
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10183655	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs17039525	0.85[ASN][1000 genomes]
rs17045199	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.85[ASN][1000 genomes]
rs17045452	0.82[CHB][hapmap]
rs2253760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2542575	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2542577	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2542588	0.93[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2692514	0.94[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2692516	0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2692534	0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2909261	0.95[ASN][1000 genomes]
rs2909459	0.82[CHB][hapmap]
rs3095756	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35487539	0.86[ASN][1000 genomes]
rs3731967	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs3770407	0.91[CHD][hapmap]
rs58359565	0.87[ASN][1000 genomes]
rs62137566	0.80[ASN][1000 genomes]
rs6746965	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs698853	0.96[ASN][1000 genomes]
rs698855	0.91[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap]
rs7583622	0.86[CHB][hapmap];0.98[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs766075	0.86[CHB][hapmap]
rs805310	0.82[CHB][hapmap]
rs805321	0.91[CHB][hapmap]
rs805328	0.95[CHB][hapmap]
rs805351	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs805352	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805365	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805386	0.91[CHB][hapmap]
rs805399	0.91[CHB][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap]
rs805401	0.91[CHB][hapmap]
rs805404	0.91[CHB][hapmap];0.80[GIH][hapmap];0.80[JPT][hapmap]
rs805408	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs805416	0.87[EUR][1000 genomes]
rs805426	0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2542571	PSME4	cis	cerebellum	SCAN
rs2542571	PSME4	cis	lymphoblastoid	seeQTL
rs2542571	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	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
3	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
4	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:54016400-54043000	Weak transcription	Gastric	stomach
8	chr2:54020200-54046200	Weak transcription	Colonic Mucosa	Colon
9	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:54020600-54048600	Strong transcription	Osteobl	bone
12	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
17	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:54021400-54047000	Strong transcription	Fetal Thymus	thymus
20	chr2:54021600-54046400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:54021800-54047600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:54022000-54044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:54022000-54047000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr2:54022000-54047000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:54022000-54047200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:54022000-54047600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:54022200-54046200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:54022200-54046600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:54022200-54047200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:54024200-54043400	Strong transcription	Dnd41	blood
32	chr2:54024800-54045400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
34	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:54027200-54046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:54028400-54044600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:54029400-54042800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:54030200-54047200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
40	chr2:54031000-54043400	Strong transcription	Adipose Nuclei	Adipose
41	chr2:54031400-54042600	Strong transcription	HepG2	liver
42	chr2:54031400-54047200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:54031600-54042200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:54031600-54043600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:54031800-54042800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:54031800-54044000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:54031800-54045600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:54032200-54043800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:54032200-54043800	Strong transcription	Brain Germinal Matrix	brain
50	chr2:54032800-54046800	Strong transcription	Primary B cells from cord blood	blood

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