Variant report

Variant	rs2692516
Chromosome Location	chr2:54027845-54027846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54025483..54027940-chr2:54030196..54032461,2	K562	blood:
2	chr2:54012138..54014028-chr2:54027548..54031166,3	K562	blood:

Variant related genes	Relation type
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10183655	0.83[CHB][hapmap]
rs10490468	0.80[MEX][hapmap]
rs17039525	0.91[ASN][1000 genomes]
rs17045199	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17045452	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs2009144	0.81[ASN][1000 genomes]
rs2253760	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2542571	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]
rs2542575	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs2542577	0.93[ASN][1000 genomes]
rs2542582	0.83[CEU][hapmap]
rs2542589	0.88[CEU][hapmap]
rs2542591	0.92[CEU][hapmap]
rs2542592	0.92[CEU][hapmap]
rs2692514	0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2692519	0.83[CEU][hapmap];0.85[MEX][hapmap]
rs2692533	0.83[CEU][hapmap];0.81[MEX][hapmap]
rs2692534	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909261	0.89[ASN][1000 genomes]
rs2909459	0.87[CHB][hapmap]
rs3095756	0.93[ASN][1000 genomes]
rs35487539	0.91[ASN][1000 genomes]
rs3731967	0.83[CHB][hapmap]
rs3731970	0.84[ASN][1000 genomes]
rs3770407	0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs3770408	0.84[ASN][1000 genomes]
rs3770409	0.83[ASN][1000 genomes]
rs58359565	0.92[ASN][1000 genomes]
rs60282090	0.81[ASN][1000 genomes]
rs62137566	0.85[ASN][1000 genomes]
rs62139788	0.81[ASN][1000 genomes]
rs62139836	0.81[ASN][1000 genomes]
rs698853	0.90[ASN][1000 genomes]
rs698855	0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs72901209	0.81[ASN][1000 genomes]
rs72901242	0.81[ASN][1000 genomes]
rs7583622	0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7600981	0.81[ASN][1000 genomes]
rs766075	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs805310	0.87[CHB][hapmap]
rs805321	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs805328	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs805351	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs805352	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs805365	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs805386	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs805399	0.95[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs805401	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs805404	0.95[CHB][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap]
rs805408	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs805426	0.95[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs805437	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv963914	chr2:54021710-54028552	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2692516	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs2692516	PSME4	cis	lymphoblastoid	seeQTL
rs2692516	PRDXDD1P	cis	parietal	SCAN
rs2692516	ACYP2	cis	multi-tissue	Pritchard
rs2692516	ACYP2	cis	Muscle Skeletal	GTEx
rs2692516	MTIF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54029800	Weak transcription	Esophagus	oesophagus
2	chr2:54015200-54038200	Weak transcription	Small Intestine	intestine
3	chr2:54015200-54046200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:54015200-54046200	Weak transcription	Aorta	Aorta
5	chr2:54015200-54051600	Weak transcription	Stomach Mucosa	stomach
6	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:54015600-54029600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:54015600-54035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:54015600-54035800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:54015800-54028600	Weak transcription	HMEC	breast
12	chr2:54015800-54029400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:54015800-54029600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:54015800-54029800	Weak transcription	Psoas Muscle	Psoas
15	chr2:54015800-54029800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:54015800-54038400	Weak transcription	Fetal Heart	heart
17	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:54016000-54031600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:54016200-54028600	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:54016400-54043000	Weak transcription	Gastric	stomach
21	chr2:54017400-54031000	Weak transcription	Ovary	ovary
22	chr2:54020200-54029600	Weak transcription	Brain Angular Gyrus	brain
23	chr2:54020200-54046200	Weak transcription	Colonic Mucosa	Colon
24	chr2:54020600-54047200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:54020600-54048400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:54020600-54048600	Strong transcription	Osteobl	bone
27	chr2:54021000-54029200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:54021000-54030600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:54021000-54030600	Strong transcription	HepG2	liver
30	chr2:54021000-54047200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr2:54021000-54047200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:54021000-54047400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:54021000-54048000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:54021200-54030000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:54021200-54030600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:54021200-54047200	Strong transcription	Placenta	Placenta
37	chr2:54021200-54047600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:54021400-54047000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:54021400-54047000	Strong transcription	Fetal Thymus	thymus
40	chr2:54021600-54035000	Strong transcription	Liver	Liver
41	chr2:54021600-54046400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:54021800-54047600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:54022000-54029600	Strong transcription	Fetal Lung	lung
44	chr2:54022000-54029800	Strong transcription	Adipose Nuclei	Adipose
45	chr2:54022000-54030800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:54022000-54030800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:54022000-54032000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:54022000-54039400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:54022000-54044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:54022000-54047000	Strong transcription	Primary T cells fromperipheralblood	blood

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