Variant report

Variant	rs16958779
Chromosome Location	chr16:82895809-82895810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10492863	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11150504	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11150506	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11150508	0.88[MEX][hapmap]
rs11644347	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11649214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11649288	0.82[AMR][1000 genomes]
rs11861198	1.00[CHB][hapmap]
rs12448722	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16958782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958905	1.00[CHB][hapmap]
rs16958926	1.00[CHB][hapmap]
rs17673125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17740830	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17740895	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17740967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17743387	1.00[CHB][hapmap]
rs17743405	1.00[CHB][hapmap]
rs4783289	1.00[CHB][hapmap]
rs62035199	0.85[ASN][1000 genomes]
rs62035200	0.91[ASN][1000 genomes]
rs7187447	1.00[CHB][hapmap]
rs7197674	1.00[CHB][hapmap]
rs72790103	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72807851	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][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	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057341	chr16:82363800-83198907	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv542997	chr16:82363800-83198907	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1063617	chr16:82786803-83229529	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2830385	chr16:82841335-82950413	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16958779	VAT1L	cis	parietal	SCAN
rs16958779	WFDC1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82848200-82898200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:82879200-82907000	Weak transcription	Left Ventricle	heart
3	chr16:82881400-82897600	Weak transcription	HMEC	breast
4	chr16:82886200-82917000	Weak transcription	Right Ventricle	heart
5	chr16:82886400-82898000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr16:82886400-82898600	Weak transcription	Aorta	Aorta
7	chr16:82889800-82900400	Weak transcription	NHDF-Ad	bronchial
8	chr16:82891000-82907000	Weak transcription	Psoas Muscle	Psoas
9	chr16:82891600-82897200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr16:82891600-82907800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr16:82892000-82898400	Weak transcription	Fetal Muscle Leg	muscle
12	chr16:82892400-82897800	Strong transcription	HSMM	muscle
13	chr16:82892400-82898800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:82893800-82896200	Weak transcription	HSMMtube	muscle
15	chr16:82894000-82898200	Weak transcription	NHEK	skin
16	chr16:82894600-82897000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr16:82895400-82896000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr16:82895400-82897000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr16:82895600-82896000	Enhancers	Brain Cingulate Gyrus	brain
20	chr16:82895600-82896600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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