Variant report

Variant	rs3805161
Chromosome Location	chr4:122835040-122835041
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10023020	0.82[CHB][hapmap]
rs10084948	0.82[CHB][hapmap]
rs1048433	0.82[GIH][hapmap]
rs10518289	0.87[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs11721457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732666	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12510839	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs13108360	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13117282	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13119055	0.81[CHB][hapmap]
rs13119958	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13121963	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13127488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13131003	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs13133876	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13138774	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13141092	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13143218	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13145213	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs13151345	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap]
rs13152701	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs1507991	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507993	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.97[TSI][hapmap]
rs17005256	0.85[CHB][hapmap]
rs2271176	0.82[CHB][hapmap]
rs2292232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217772	0.82[CHB][hapmap]
rs3762840	0.82[CHB][hapmap]
rs3805158	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3811742	0.82[CHB][hapmap]
rs4833777	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4833778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61545746	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7672879	0.96[CEU][hapmap]
rs884701	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs906494	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906495	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs906496	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs951974	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs953691	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap]
rs9998785	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3805161	CCNA2	cis	lymphoblastoid	seeQTL
rs3805161	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs3805161	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122813400-122860600	Weak transcription	Fetal Lung	lung
2	chr4:122821600-122857400	Weak transcription	Fetal Heart	heart
3	chr4:122831200-122853200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:122834600-122835200	Enhancers	NHDF-Ad	bronchial

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