Variant report

Variant	rs2036995
Chromosome Location	chr3:111406088-111406089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13078891	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13086157	0.85[CEU][hapmap]
rs1355767	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1398747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1553970	0.92[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[MEX][hapmap];0.81[AFR][1000 genomes]
rs1606503	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2036996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35957576	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4481128	0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4682052	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.92[MEX][hapmap];0.84[AFR][1000 genomes]
rs4682292	0.84[AFR][1000 genomes]
rs4682295	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62275506	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs867293	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2036995	PLCXD2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111395800-111413400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:111396400-111406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:111396400-111408200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:111396600-111409200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:111397200-111408000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:111397200-111408200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:111399000-111409400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:111400400-111408200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:111400800-111407200	Weak transcription	Hela-S3	cervix
10	chr3:111400800-111408400	Weak transcription	HMEC	breast
11	chr3:111400800-111409000	Weak transcription	HSMMtube	muscle
12	chr3:111400800-111411800	Weak transcription	Primary B cells from cord blood	blood
13	chr3:111401000-111412000	Weak transcription	Stomach Mucosa	stomach
14	chr3:111401200-111411600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:111402200-111407200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:111402600-111409000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:111402600-111411600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:111404000-111407200	Weak transcription	Small Intestine	intestine
19	chr3:111404000-111407800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:111404000-111408200	Weak transcription	Pancreas	Pancrea
21	chr3:111404000-111409000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:111404000-111409200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:111404000-111409200	Weak transcription	Fetal Thymus	thymus
24	chr3:111404800-111406200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:111405200-111406600	Weak transcription	HepG2	liver
26	chr3:111405200-111406800	Weak transcription	A549	lung
27	chr3:111405400-111409600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:111405800-111407600	Enhancers	Fetal Intestine Small	intestine
29	chr3:111405800-111408200	Enhancers	Fetal Intestine Large	intestine
30	chr3:111406000-111406200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:111406000-111410400	Enhancers	Primary T cells from cord blood	blood

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