Variant report

Variant	rs1003873
Chromosome Location	chr4:48096781-48096782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1003872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116684	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs13150783	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs13151608	0.87[JPT][hapmap]
rs1396050	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1567217	1.00[CHB][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1911669	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2279965	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2456927	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2661525	0.82[ASN][1000 genomes]
rs2661528	0.90[TSI][hapmap]
rs2704401	0.90[TSI][hapmap]
rs2940328	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321632	0.87[JPT][hapmap]
rs62301688	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1003873	JPH1	trans	cerebellum	SCAN
rs1003873	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48067600-48102400	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr4:48070800-48105200	Weak transcription	GM12878-XiMat	blood
3	chr4:48083000-48098000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:48083000-48098200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr4:48083400-48098200	Strong transcription	Primary T cells from cord blood	blood
6	chr4:48084400-48098000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr4:48084600-48101600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:48085200-48102400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:48086400-48099000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:48088600-48104000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:48088600-48106000	Weak transcription	Fetal Thymus	thymus
12	chr4:48088600-48107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:48088800-48105200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:48090000-48100800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:48090800-48098600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:48091600-48101000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:48092400-48098200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:48092600-48097200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:48092600-48098400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:48092800-48098200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:48094000-48096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:48094800-48096800	Enhancers	HMEC	breast
23	chr4:48094800-48097200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:48094800-48097200	Enhancers	Hela-S3	cervix
25	chr4:48095000-48097000	Enhancers	NHEK	skin
26	chr4:48095200-48096800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:48095400-48097000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:48095400-48097000	Enhancers	HUVEC	blood vessel
29	chr4:48095600-48096800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:48095800-48096800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:48096200-48096800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:48096600-48096800	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr4:48096600-48096800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:48096600-48097800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:48096600-48097800	Weak transcription	Rectal Mucosa Donor 31	rectum

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