Variant report

Variant	rs4481128
Chromosome Location	chr3:111405407-111405408
allele	G/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	GATA3	chr3:111405114-111405717	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr3:111405095-111405742	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
PLCXD2	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1398747	0.81[EUR][1000 genomes]
rs1513331	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2036995	0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2036996	0.83[EUR][1000 genomes]
rs4481129	1.00[ASN][1000 genomes]
rs62275506	0.81[EUR][1000 genomes]
rs7651713	0.94[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs867293	0.81[EUR][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
rs4481128	PLCXD2	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr3:111401600-111405800	Weak transcription	Fetal Intestine Large	intestine
16	chr3:111401800-111405800	Weak transcription	Fetal Intestine Small	intestine
17	chr3:111402200-111407200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:111402600-111409000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:111402600-111411600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:111404000-111407200	Weak transcription	Small Intestine	intestine
21	chr3:111404000-111407800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:111404000-111408200	Weak transcription	Pancreas	Pancrea
23	chr3:111404000-111409000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:111404000-111409200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:111404000-111409200	Weak transcription	Fetal Thymus	thymus
26	chr3:111404800-111406200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:111405000-111406000	Weak transcription	Primary T cells from cord blood	blood
28	chr3:111405200-111406600	Weak transcription	HepG2	liver
29	chr3:111405200-111406800	Weak transcription	A549	lung
30	chr3:111405400-111409600	Weak transcription	Primary hematopoietic stem cells	blood

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