Variant report

Variant	rs13143218
Chromosome Location	chr4:122820075-122820076
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10023020	0.96[CHB][hapmap];0.87[JPT][hapmap]
rs10024820	0.81[ASN][1000 genomes]
rs10084948	0.96[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1048433	0.82[CHB][hapmap]
rs10518289	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs11721457	0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11732666	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733882	0.81[ASN][1000 genomes]
rs12510839	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs13108360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13117282	0.93[EUR][1000 genomes]
rs13119055	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs13119958	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121963	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13127488	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13131003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13133876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13138774	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141092	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13145213	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs13151345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs13152701	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1507991	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1507993	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs17005256	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2271176	0.96[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2292232	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3217772	0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs35495505	0.84[ASN][1000 genomes]
rs3762840	0.96[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3805158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805161	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811742	0.96[CHB][hapmap];0.87[JPT][hapmap]
rs4833233	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4833236	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4833777	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833778	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61545746	0.89[EUR][1000 genomes]
rs67775544	0.84[ASN][1000 genomes]
rs6845901	0.80[ASN][1000 genomes]
rs7672879	1.00[CEU][hapmap]
rs769236	0.81[ASN][1000 genomes]
rs884701	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs906494	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs906495	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs906496	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs951974	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs953691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs9995319	0.81[ASN][1000 genomes]
rs9998785	0.96[CHB][hapmap];0.87[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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1803127	chr4:122806228-122830334	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1014729	chr4:122806228-122848966	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13143218	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs13143218	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122813400-122860600	Weak transcription	Fetal Lung	lung
2	chr4:122819600-122821200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:122819800-122821400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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