Variant report

Variant	rs3744372
Chromosome Location	chr17:33802156-33802157
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12449487	0.82[EUR][1000 genomes]
rs12451876	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12936256	0.82[EUR][1000 genomes]
rs12936954	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12937961	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12939675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949245	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12953115	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2304967	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34121367	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34620580	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34646901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34656640	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34734788	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34747751	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34787927	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35057074	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35210090	0.82[EUR][1000 genomes]
rs35367381	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35563348	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35863546	0.82[EUR][1000 genomes]
rs4239251	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs55668225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56033496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56061417	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56845839	0.88[ASN][1000 genomes]
rs57580463	0.90[ASN][1000 genomes]
rs60191377	0.88[ASN][1000 genomes]
rs67338337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67536209	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72825999	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72826000	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8064887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064988	0.89[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs8065289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066132	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8069360	0.90[ASN][1000 genomes]
rs8072477	0.83[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8076783	0.90[ASN][1000 genomes]
rs8079653	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1056116	chr17:33691457-33815452	Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3432530	chr17:33738621-33802241	Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3744372	EFCAB5	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33796000-33803000	Weak transcription	Fetal Thymus	thymus
2	chr17:33800400-33807200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:33800400-33809400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:33800600-33803200	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr17:33800800-33802400	Strong transcription	Fetal Lung	lung
6	chr17:33800800-33803600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:33800800-33804200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:33800800-33807200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr17:33801000-33802600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr17:33801000-33803400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr17:33801000-33804400	ZNF genes & repeats	Primary T cells from cord blood	blood
12	chr17:33801000-33805200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr17:33801200-33802200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr17:33801200-33804000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:33801200-33804200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:33801200-33804200	Strong transcription	Dnd41	blood
17	chr17:33801800-33809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:33802000-33803400	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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