Variant report

Variant	rs2542583
Chromosome Location	chr2:54009319-54009320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54009276-54009476	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:54003379..54005781-chr2:54007971..54009491,2	K562	blood:
2	chr2:54008638..54010431-chr2:54015192..54016791,2	K562	blood:
3	chr2:54005450..54009450-chr2:54009767..54014218,9	K562	blood:
4	chr2:54008226..54010680-chr2:54013442..54015348,3	MCF-7	breast:

Variant related genes	Relation type
ERLEC1	TF binding region
ENSG00000115239	Chromatin interaction
ENSG00000068912	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10490468	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11897282	0.82[ASN][1000 genomes]
rs13408029	0.82[ASN][1000 genomes]
rs17045176	0.80[ASN][1000 genomes]
rs17045203	0.91[ASN][1000 genomes]
rs17520505	0.81[ASN][1000 genomes]
rs17521008	0.81[ASN][1000 genomes]
rs2287340	0.88[ASN][1000 genomes]
rs2302797	0.82[ASN][1000 genomes]
rs2542572	0.83[ASN][1000 genomes]
rs2542573	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2542581	0.83[ASN][1000 genomes]
rs2542582	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542589	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542590	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542591	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542592	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2692512	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2692513	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2692519	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692521	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2692522	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2692530	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2692533	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692534	0.82[AMR][1000 genomes]
rs2692535	0.86[ASN][1000 genomes]
rs2909262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2949813	0.86[ASN][1000 genomes]
rs35772199	0.81[ASN][1000 genomes]
rs3770394	0.82[ASN][1000 genomes]
rs3770395	0.82[ASN][1000 genomes]
rs3770397	0.80[ASN][1000 genomes]
rs3770399	0.82[ASN][1000 genomes]
rs4116709	0.81[ASN][1000 genomes]
rs55897904	0.89[ASN][1000 genomes]
rs58326257	0.89[ASN][1000 genomes]
rs62137573	0.81[ASN][1000 genomes]
rs62137602	0.80[ASN][1000 genomes]
rs62137606	0.82[ASN][1000 genomes]
rs62137610	0.86[ASN][1000 genomes]
rs62137611	0.86[ASN][1000 genomes]
rs62137612	0.91[ASN][1000 genomes]
rs6730006	0.82[ASN][1000 genomes]
rs719127	0.82[ASN][1000 genomes]
rs72901256	0.84[ASN][1000 genomes]
rs7600817	0.82[ASN][1000 genomes]
rs805437	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2542583	PSME4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
3	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
5	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
8	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
9	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
10	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:53996000-54011000	Weak transcription	Fetal Brain Male	brain
14	chr2:53996000-54011200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:53996000-54011600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:53996000-54011600	Weak transcription	Fetal Lung	lung
17	chr2:53996000-54011800	Weak transcription	NHDF-Ad	bronchial
18	chr2:53996200-54009800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:53996200-54011000	Weak transcription	Brain Angular Gyrus	brain
20	chr2:53996200-54011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:53996200-54012600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:53996400-54009400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:53996400-54011000	Weak transcription	NHEK	skin
24	chr2:53996400-54011200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:53996400-54011200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:53996400-54011200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:53996400-54011400	Weak transcription	Thymus	Thymus
28	chr2:53996400-54011600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:53996400-54011800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:53996400-54011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:53996400-54012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:53996400-54012400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:53996600-54010600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:53996600-54011400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:53996800-54010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:53996800-54011200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:53997000-54010800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:53997000-54011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:53997000-54011600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:53997200-54010600	Weak transcription	Hela-S3	cervix
41	chr2:53998200-54010600	Weak transcription	HepG2	liver
42	chr2:53998800-54011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:54000800-54009600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:54002200-54010400	Strong transcription	Fetal Thymus	thymus
45	chr2:54002400-54009600	Weak transcription	NHLF	lung
46	chr2:54002800-54011200	Weak transcription	HMEC	breast
47	chr2:54002800-54011400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr2:54003400-54011400	Weak transcription	Fetal Heart	heart
49	chr2:54003800-54010000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:54004000-54012600	Weak transcription	Small Intestine	intestine

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