Variant report

Variant	rs2692533
Chromosome Location	chr2:54007171-54007172
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54006024..54008035-chr2:54009628..54012351,2	K562	blood:
2	chr2:54005450..54009450-chr2:54009767..54014218,9	K562	blood:
3	chr2:53993911..53997608-chr2:54000470..54007207,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143942	Chromatin interaction
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10490468	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11897282	0.92[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs11901698	0.92[CHB][hapmap];0.80[JPT][hapmap];0.84[YRI][hapmap]
rs1232	0.92[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs13408029	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17045176	0.92[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs17045199	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs17045203	0.92[CHB][hapmap];0.96[CHD][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs17520505	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs17521008	0.85[CHD][hapmap];0.86[MKK][hapmap];0.80[ASN][1000 genomes]
rs2287340	0.92[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs2302797	0.92[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.86[MKK][hapmap];0.81[ASN][1000 genomes]
rs2542572	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2542573	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2542581	0.81[CHD][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap]
rs2542582	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542583	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542589	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542590	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542591	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542592	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2543629	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs2692512	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692513	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692516	0.83[CEU][hapmap];0.81[MEX][hapmap]
rs2692519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692521	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2692522	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2692530	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2692534	0.92[CEU][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs2692535	0.82[ASN][1000 genomes]
rs2909262	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2949813	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3770394	0.92[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770395	0.81[ASN][1000 genomes]
rs3770397	0.84[ASN][1000 genomes]
rs3770399	0.81[ASN][1000 genomes]
rs3770411	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs4116709	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs55897904	0.88[ASN][1000 genomes]
rs58326257	0.88[ASN][1000 genomes]
rs62137573	0.80[ASN][1000 genomes]
rs62137602	0.84[ASN][1000 genomes]
rs62137606	0.81[ASN][1000 genomes]
rs62137610	0.90[ASN][1000 genomes]
rs62137611	0.90[ASN][1000 genomes]
rs62137612	0.88[ASN][1000 genomes]
rs719127	0.92[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs72901256	0.80[ASN][1000 genomes]
rs7600817	0.81[ASN][1000 genomes]
rs805316	0.83[ASW][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs805334	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs805338	0.92[CHB][hapmap]
rs805437	0.92[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs805446	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs805447	0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2692533	PSME4	cis	lymphoblastoid	seeQTL
rs2692533	ACYP2	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53995600-54007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:53995600-54007400	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:53995600-54007800	Weak transcription	Placenta	Placenta
4	chr2:53995600-54008400	Weak transcription	Ovary	ovary
5	chr2:53995600-54009000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:53995600-54009000	Weak transcription	Lung	lung
7	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
9	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
11	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:53995800-54008600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
15	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
16	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
17	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:53996000-54009000	Weak transcription	Brain Substantia Nigra	brain
21	chr2:53996000-54011000	Weak transcription	Fetal Brain Male	brain
22	chr2:53996000-54011200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:53996000-54011600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:53996000-54011600	Weak transcription	Fetal Lung	lung
25	chr2:53996000-54011800	Weak transcription	NHDF-Ad	bronchial
26	chr2:53996200-54007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:53996200-54009800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:53996200-54011000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:53996200-54011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:53996200-54012600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:53996400-54007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:53996400-54009000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:53996400-54009000	Weak transcription	Brain Germinal Matrix	brain
34	chr2:53996400-54009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:53996400-54009400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:53996400-54011000	Weak transcription	NHEK	skin
37	chr2:53996400-54011200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:53996400-54011200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:53996400-54011200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:53996400-54011400	Weak transcription	Thymus	Thymus
41	chr2:53996400-54011600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:53996400-54011800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:53996400-54011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:53996400-54012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:53996400-54012400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:53996600-54010600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:53996600-54011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:53996800-54007200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:53996800-54010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:53996800-54011200	Weak transcription	Duodenum Mucosa	Duodenum

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