Variant report

Variant	rs805438
Chromosome Location	chr2:54056188-54056189
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54054213..54056841-chr2:54086563..54088065,2	K562	blood:

Variant related genes	Relation type
ENSG00000270898	Chromatin interaction
ENSG00000119737	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10171954	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10178643	0.82[ASN][1000 genomes]
rs10188142	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10192626	0.86[ASN][1000 genomes]
rs10201938	0.83[ASN][1000 genomes]
rs10203095	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10490471	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11684084	0.84[CEU][hapmap]
rs12621225	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs13414216	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13417926	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13432632	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2111622	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2111623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2111868	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2160929	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2160930	0.84[TSI][hapmap]
rs2160931	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2193682	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2357693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2542574	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2542576	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2542579	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2542585	1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2542588	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs2542593	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2692515	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692518	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692531	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2692536	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2692537	0.81[ASN][1000 genomes]
rs2909263	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2949811	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2949812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821081	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4413193	0.81[EUR][1000 genomes]
rs4671529	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4671583	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs56173218	0.81[ASN][1000 genomes]
rs6705712	0.91[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs6708095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs6724389	0.82[CEU][hapmap]
rs6738369	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743627	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs698854	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs698858	0.84[EUR][1000 genomes]
rs718872	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7556791	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7557799	0.81[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7557898	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs7569214	0.89[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs7569370	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs7572776	0.84[ASN][1000 genomes]
rs7573991	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7596349	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7601692	0.93[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805308	0.85[CEU][hapmap]
rs805309	0.88[CEU][hapmap]
rs805322	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[LWK][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs805341	0.92[CEU][hapmap];0.83[MEX][hapmap]
rs805359	0.92[EUR][1000 genomes]
rs805366	0.84[EUR][1000 genomes]
rs805367	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs805373	0.86[GIH][hapmap];0.92[MEX][hapmap]
rs805374	0.92[CEU][hapmap];0.90[GIH][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs805375	0.92[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs805379	0.91[EUR][1000 genomes]
rs805380	0.92[EUR][1000 genomes]
rs805391	0.90[EUR][1000 genomes]
rs805392	0.89[EUR][1000 genomes]
rs805393	0.86[EUR][1000 genomes]
rs805402	0.91[EUR][1000 genomes]
rs805405	0.88[EUR][1000 genomes]
rs805410	0.93[CEU][hapmap];0.86[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs805421	0.87[EUR][1000 genomes]
rs805423	0.96[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs805424	0.93[EUR][1000 genomes]
rs805430	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs805433	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs805436	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs805439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs805441	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805450	0.96[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs805453	0.84[EUR][1000 genomes]
rs809280	0.92[EUR][1000 genomes]
rs918207	0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs805438	PSME4	cis	lymphoblastoid	seeQTL
rs805438	ACYP2	cis	Muscle Skeletal	GTEx
rs805438	ACYP2	cis	multi-tissue	Pritchard
rs805438	C2orf73	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
2	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
4	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
6	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
8	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
13	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
15	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:54047000-54080200	Weak transcription	A549	lung
17	chr2:54047000-54080400	Weak transcription	Gastric	stomach
18	chr2:54047000-54080400	Weak transcription	Pancreas	Pancrea
19	chr2:54047000-54080800	Weak transcription	Aorta	Aorta
20	chr2:54047200-54056800	Weak transcription	HSMMtube	muscle
21	chr2:54047200-54059600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:54047200-54061800	Weak transcription	Thymus	Thymus
23	chr2:54047200-54063000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:54047200-54067600	Weak transcription	HSMM	muscle
25	chr2:54047200-54070800	Weak transcription	Placenta	Placenta
26	chr2:54047200-54077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:54047200-54080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:54047200-54080200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:54047200-54080200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:54047200-54080200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:54047200-54080400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:54047200-54080400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:54047200-54080800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:54047600-54058400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:54047600-54080400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:54047600-54080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:54047800-54064200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:54048200-54065000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:54050200-54080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:54050400-54080200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:54050600-54080200	Weak transcription	Fetal Stomach	stomach
42	chr2:54051000-54080000	Weak transcription	Osteobl	bone
43	chr2:54052800-54056200	Enhancers	Brain Substantia Nigra	brain
44	chr2:54053000-54057200	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:54053000-54057200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:54054000-54057000	Enhancers	Brain Anterior Caudate	brain
47	chr2:54054000-54066400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:54054000-54080400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:54054400-54063000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:54054400-54080400	Weak transcription	NHLF	lung

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