Variant report

Variant	rs1152481
Chromosome Location	chr14:56783989-56783990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1028972	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1152473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1152474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152475	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1152476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152483	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1152487	0.84[ASN][1000 genomes]
rs1152490	0.81[ASN][1000 genomes]
rs1152491	0.82[ASN][1000 genomes]
rs1188692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1479752	0.98[EUR][1000 genomes]
rs171411	0.87[EUR][1000 genomes]
rs1979420	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs242385	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs242393	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs242395	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[MEX][hapmap];0.94[EUR][1000 genomes]
rs242398	0.90[CEU][hapmap];0.94[MEX][hapmap];0.94[EUR][1000 genomes]
rs242406	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs242407	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[EUR][1000 genomes]
rs242410	1.00[CEU][hapmap];0.94[MEX][hapmap];0.94[EUR][1000 genomes]
rs242414	0.91[EUR][1000 genomes]
rs242417	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs242419	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[EUR][1000 genomes]
rs242579	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs242587	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs242588	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242592	1.00[CEU][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs242593	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs242594	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34175054	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs375156	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs3783668	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.94[EUR][1000 genomes]
rs402332	0.94[EUR][1000 genomes]
rs429676	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6573087	0.89[EUR][1000 genomes]
rs7140808	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs7145410	0.82[EUR][1000 genomes]
rs7153057	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs7153858	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs753109	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs754689	1.00[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.93[EUR][1000 genomes]
rs754690	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.94[EUR][1000 genomes]
rs899603	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1044886	chr14:56689682-56834648	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv542104	chr14:56689682-56834648	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv901978	chr14:56740554-56799997	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv901979	chr14:56740554-56802610	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1152481	SEMA3A	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56764400-56785600	Weak transcription	Lung	lung
2	chr14:56764400-56798200	Weak transcription	Pancreas	Pancrea
3	chr14:56764400-56808800	Weak transcription	Thymus	Thymus
4	chr14:56768600-56784600	Weak transcription	Dnd41	blood
5	chr14:56774400-56806400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:56778400-56797200	Weak transcription	Ovary	ovary
7	chr14:56780800-56791400	Weak transcription	Fetal Brain Female	brain
8	chr14:56781000-56784400	Weak transcription	Primary T cells from cord blood	blood
9	chr14:56781000-56785200	Weak transcription	Fetal Intestine Small	intestine
10	chr14:56782800-56784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr14:56783200-56797200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr14:56783600-56786800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr14:56783800-56793400	Weak transcription	Aorta	Aorta

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