Variant report

Variant	rs951974
Chromosome Location	chr4:122828794-122828795
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10001889	0.89[AFR][1000 genomes]
rs10004284	0.89[AFR][1000 genomes]
rs10007956	0.89[AFR][1000 genomes]
rs10013916	0.80[AFR][1000 genomes]
rs10023020	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes]
rs10028375	0.83[AFR][1000 genomes]
rs10084948	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes]
rs1048433	1.00[ASW][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.84[AFR][1000 genomes]
rs10518289	0.91[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs11098643	0.89[AFR][1000 genomes]
rs11721457	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11724322	0.80[AFR][1000 genomes]
rs11732666	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734075	0.89[AFR][1000 genomes]
rs12510839	1.00[ASW][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.89[AFR][1000 genomes]
rs13106764	0.89[AFR][1000 genomes]
rs13108360	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13108419	0.89[AFR][1000 genomes]
rs13113421	0.89[AFR][1000 genomes]
rs13117282	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13119055	0.91[CHB][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13119958	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121963	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13127488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13128434	0.89[AFR][1000 genomes]
rs13130789	0.89[AFR][1000 genomes]
rs13131003	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs13133876	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138774	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13140070	0.89[AFR][1000 genomes]
rs13141092	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13143218	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]
rs13145213	0.91[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.80[ASN][1000 genomes]
rs13151345	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs13152701	1.00[ASW][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1507991	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs17005256	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2271176	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2292232	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28435300	0.89[AFR][1000 genomes]
rs28522256	0.89[AFR][1000 genomes]
rs28672860	0.89[AFR][1000 genomes]
rs3217772	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.89[AFR][1000 genomes]
rs34445121	0.89[AFR][1000 genomes]
rs35341163	0.80[AFR][1000 genomes]
rs35495505	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3762840	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes]
rs3805158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805161	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]
rs3811742	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4075065	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes]
rs4075066	0.89[AFR][1000 genomes]
rs4240262	0.89[AFR][1000 genomes]
rs4240263	0.89[AFR][1000 genomes]
rs4240264	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes]
rs4833232	0.89[AFR][1000 genomes]
rs4833233	0.81[JPT][hapmap]
rs4833234	0.89[AFR][1000 genomes]
rs4833235	0.89[AFR][1000 genomes]
rs4833236	0.89[CHB][hapmap];0.89[JPT][hapmap];0.80[AFR][1000 genomes]
rs4833773	0.89[AFR][1000 genomes]
rs4833775	0.89[AFR][1000 genomes]
rs4833777	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4833778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61545746	0.90[EUR][1000 genomes]
rs67150579	0.89[AFR][1000 genomes]
rs67775544	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6822155	0.89[AFR][1000 genomes]
rs7672879	0.95[CEU][hapmap]
rs7676867	0.83[AFR][1000 genomes]
rs769236	0.89[AFR][1000 genomes]
rs7699289	0.89[AFR][1000 genomes]
rs884701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906494	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs906495	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs906496	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap]
rs953691	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs966555	0.80[AFR][1000 genomes]
rs9993206	1.00[ASW][hapmap];0.89[AFR][1000 genomes]
rs9995319	0.89[AFR][1000 genomes]
rs9998785	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[AFR][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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs951974	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs951974	CCNA2	cis	lymphoblastoid	seeQTL
rs951974	BBS7	cis	cerebellum	SCAN
rs951974	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs951974	BBS7	cis	parietal	SCAN

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	chr4:122821600-122857400	Weak transcription	Fetal Heart	heart
3	chr4:122827200-122829800	Weak transcription	Psoas Muscle	Psoas

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