Variant report

Variant	rs698853
Chromosome Location	chr2:54053872-54053873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10183655	0.83[CHB][hapmap]
rs17039525	0.87[ASN][1000 genomes]
rs17045199	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs2253760	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs2542571	0.84[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.96[ASN][1000 genomes]
rs2542575	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2542577	0.94[ASN][1000 genomes]
rs2692514	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs2692516	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[ASN][1000 genomes]
rs2692534	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2909261	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095756	0.94[ASN][1000 genomes]
rs35487539	0.86[ASN][1000 genomes]
rs3731967	0.83[CHB][hapmap]
rs3770407	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs58359565	0.88[ASN][1000 genomes]
rs62137566	0.80[ASN][1000 genomes]
rs698855	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7583622	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs766075	0.91[CHB][hapmap]
rs805321	0.86[CHB][hapmap]
rs805328	0.90[CHB][hapmap]
rs805351	0.86[CHB][hapmap]
rs805352	0.86[CHB][hapmap]
rs805365	0.86[CHB][hapmap]
rs805386	0.86[CHB][hapmap]
rs805399	0.86[CHB][hapmap]
rs805401	0.86[CHB][hapmap]
rs805404	0.86[CHB][hapmap]
rs805408	0.86[CHB][hapmap]
rs805426	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs698853	PSME4	cis	cerebellum	SCAN
rs698853	PSME4	cis	lymphoblastoid	seeQTL
rs698853	ACYP2	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
4	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
6	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
7	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
8	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
10	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
12	chr2:54046800-54054000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:54046800-54054200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:54046800-54054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
17	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:54047000-54054000	Weak transcription	NHLF	lung
20	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
21	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
23	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:54047000-54080200	Weak transcription	A549	lung
25	chr2:54047000-54080400	Weak transcription	Gastric	stomach
26	chr2:54047000-54080400	Weak transcription	Pancreas	Pancrea
27	chr2:54047000-54080800	Weak transcription	Aorta	Aorta
28	chr2:54047200-54054000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:54047200-54054200	Weak transcription	Left Ventricle	heart
30	chr2:54047200-54054600	Weak transcription	Lung	lung
31	chr2:54047200-54055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:54047200-54056800	Weak transcription	HSMMtube	muscle
33	chr2:54047200-54059600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:54047200-54061800	Weak transcription	Thymus	Thymus
35	chr2:54047200-54063000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:54047200-54067600	Weak transcription	HSMM	muscle
37	chr2:54047200-54070800	Weak transcription	Placenta	Placenta
38	chr2:54047200-54077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:54047200-54080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:54047200-54080200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:54047200-54080200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:54047200-54080200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr2:54047200-54080400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:54047200-54080400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:54047200-54080800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr2:54047400-54054600	Weak transcription	Primary T cells from cord blood	blood
47	chr2:54047400-54055800	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:54047600-54054600	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:54047600-54058400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:54047600-54080400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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