Variant report

Variant	rs13410389
Chromosome Location	chr2:113738023-113738024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10173618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10196340	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10200415	0.91[ASN][1000 genomes]
rs10496447	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs10864909	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12711746	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13392494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13407838	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13415097	0.91[EUR][1000 genomes]
rs1374284	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1446516	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17042691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17607787	1.00[CEU][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17659543	0.91[EUR][1000 genomes]
rs17660913	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs28938790	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28947168	0.99[EUR][1000 genomes]
rs28947170	0.84[EUR][1000 genomes]
rs28947203	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28954071	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28954077	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28993969	0.96[EUR][1000 genomes]
rs3768769	0.81[EUR][1000 genomes]
rs56198490	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6542107	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6542108	0.91[ASN][1000 genomes]
rs6542109	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6714534	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7571656	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]

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	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv961489	chr2:113737947-113742104	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13410389	ZC3H8	cis	parietal	SCAN
rs13410389	SLC35F5	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113733800-113739200	Enhancers	Primary T cells from cord blood	blood
2	chr2:113735200-113739000	Enhancers	Fetal Thymus	thymus
3	chr2:113736000-113747400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:113736800-113738600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr2:113736800-113738600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr2:113736800-113738600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr2:113737000-113738400	Enhancers	GM12878-XiMat	blood
8	chr2:113737000-113739200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:113737400-113738400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:113737400-113738400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr2:113737400-113738400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:113737400-113738600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:113737400-113742400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:113737600-113742600	Weak transcription	Thymus	Thymus
15	chr2:113738000-113739200	Enhancers	Primary T cells fromperipheralblood	blood

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