Variant report

Variant	rs2542581
Chromosome Location	chr2:54002064-54002065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54000755..54005872-chr2:54012660..54015787,4	MCF-7	breast:
2	chr2:54000281..54003066-chr2:54012405..54016075,3	K562	blood:
3	chr2:53993911..53997608-chr2:54000470..54007207,10	MCF-7	breast:

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

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10490468	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs11897282	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11901698	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13408029	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17039530	0.81[CHB][hapmap]
rs17045203	0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs17520505	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17521008	1.00[ASW][hapmap];0.96[GIH][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2008082	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2287340	0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs2302797	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2542572	0.93[CEU][hapmap];0.81[CHB][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2542578	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2542580	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2542582	0.82[MKK][hapmap];0.80[ASN][1000 genomes]
rs2542583	0.83[ASN][1000 genomes]
rs2543629	0.90[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2692519	0.84[CHD][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap]
rs2692523	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2692530	0.81[ASN][1000 genomes]
rs2692533	0.81[CHD][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap]
rs2692535	0.82[AFR][1000 genomes]
rs2909262	0.82[ASN][1000 genomes]
rs2949813	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs35772199	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3731970	0.83[YRI][hapmap]
rs3770399	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3770407	0.83[YRI][hapmap]
rs3770411	0.89[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.86[TSI][hapmap];0.83[YRI][hapmap]
rs3922262	0.81[ASN][1000 genomes]
rs4116709	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55897904	0.83[ASN][1000 genomes]
rs56214822	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58326257	0.85[ASN][1000 genomes]
rs62137565	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62137566	0.81[AMR][1000 genomes]
rs62137573	0.80[AFR][1000 genomes]
rs62137602	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62137610	0.80[ASN][1000 genomes]
rs62137611	0.80[ASN][1000 genomes]
rs62137612	0.88[ASN][1000 genomes]
rs6730006	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs719127	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72901256	0.80[AFR][1000 genomes]
rs7558968	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7583622	0.89[CEU][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs805435	0.82[AMR][1000 genomes];0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2542581	PDDC1	trans	cerebellum	SCAN
rs2542581	RAE1	trans	cerebellum	SCAN
rs2542581	PSME4	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53995400-54003600	Weak transcription	Small Intestine	intestine
2	chr2:53995600-54005800	Weak transcription	HSMM	muscle
3	chr2:53995600-54007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:53995600-54007400	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:53995600-54007800	Weak transcription	Placenta	Placenta
6	chr2:53995600-54008400	Weak transcription	Ovary	ovary
7	chr2:53995600-54009000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:53995600-54009000	Weak transcription	Lung	lung
9	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
11	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
13	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:53995800-54003000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:53995800-54006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:53995800-54008600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
19	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
20	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
21	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:53996000-54004400	Weak transcription	Osteobl	bone
25	chr2:53996000-54005800	Weak transcription	Liver	Liver
26	chr2:53996000-54006800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:53996000-54009000	Weak transcription	Brain Substantia Nigra	brain
28	chr2:53996000-54011000	Weak transcription	Fetal Brain Male	brain
29	chr2:53996000-54011200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:53996000-54011600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:53996000-54011600	Weak transcription	Fetal Lung	lung
32	chr2:53996000-54011800	Weak transcription	NHDF-Ad	bronchial
33	chr2:53996200-54003000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr2:53996200-54003600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:53996200-54004400	Weak transcription	Primary B cells from cord blood	blood
36	chr2:53996200-54006400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:53996200-54006800	Weak transcription	NH-A	brain
38	chr2:53996200-54007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:53996200-54009800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:53996200-54011000	Weak transcription	Brain Angular Gyrus	brain
41	chr2:53996200-54011400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:53996200-54012600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:53996400-54003000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:53996400-54003200	Weak transcription	Primary T cells from cord blood	blood
45	chr2:53996400-54007000	Weak transcription	Fetal Brain Female	brain
46	chr2:53996400-54007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:53996400-54009000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:53996400-54009000	Weak transcription	Brain Germinal Matrix	brain
49	chr2:53996400-54009200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:53996400-54009400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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