Variant report

Variant	rs8050643
Chromosome Location	chr16:82958163-82958164
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr16:82957919-82958249	GM12878	blood:	n/a	chr16:82958057-82958074 chr16:82958096-82958111 chr16:82958065-82958074 chr16:82958065-82958074 chr16:82958066-82958081
2	ZNF263	chr16:82957874-82958436	HEK293-T-REx	kidney:	n/a	chr16:82958244-82958265
3	TCF7L2	chr16:82957385-82958697	HEK293	kidney:	n/a	chr16:82957827-82957843 chr16:82957827-82957843 chr16:82957829-82957839 chr16:82957831-82957840 chr16:82957828-82957842
4	KAP1	chr16:82957989-82958511	HEK293	kidney:	n/a	n/a
5	KAP1	chr16:82958092-82958672	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
CDH13	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1008648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150522	0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs11150523	0.88[ASN][1000 genomes]
rs12102479	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12919606	0.88[ASN][1000 genomes]
rs12923557	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs13331478	0.88[CEU][hapmap];0.88[ASN][1000 genomes]
rs16958850	0.88[CEU][hapmap];0.88[ASN][1000 genomes]
rs16958852	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs16958858	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs17673003	1.00[CHB][hapmap]
rs17675094	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs17743051	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991028	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2011228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011241	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216734	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216735	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2216736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2325691	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417188	0.88[ASN][1000 genomes]
rs28457841	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661446	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28701026	0.82[EUR][1000 genomes]
rs34482883	0.88[ASN][1000 genomes]
rs35775260	0.88[ASN][1000 genomes]
rs3848298	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273031	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312297	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4485359	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569269	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4584813	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4616278	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635337	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4782737	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4782738	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4783299	0.88[ASN][1000 genomes]
rs4783300	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs62037203	1.00[ASN][1000 genomes]
rs6565078	0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs7187633	0.84[ASN][1000 genomes]
rs7190538	0.84[ASN][1000 genomes]
rs7404932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7404959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7501309	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046347	0.89[ASN][1000 genomes]
rs8050659	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9319579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923309	0.86[ASN][1000 genomes]
rs9926654	0.88[ASN][1000 genomes]
rs9928115	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930233	1.00[CHB][hapmap]
rs9936335	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9940486	0.92[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941054	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9941327	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs995506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	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
2	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
3	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
4	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
5	nsv907028	chr16:82940611-82974628	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv907029	chr16:82951179-83044665	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	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
rs8050643	C16orf61	cis	parietal	SCAN
rs8050643	COTL1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82926800-82961200	Weak transcription	HSMM	muscle
2	chr16:82934000-83003400	Weak transcription	NHEK	skin
3	chr16:82934400-82967000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:82934400-82967400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr16:82934600-82989600	Weak transcription	HSMMtube	muscle
6	chr16:82948400-82958800	Weak transcription	Left Ventricle	heart
7	chr16:82954200-82960400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:82957400-82958200	Enhancers	Brain Hippocampus Middle	brain
9	chr16:82957400-82959200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr16:82957800-82958400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr16:82957800-82959600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr16:82957800-82959600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:82957800-82960200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr16:82958000-82958200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr16:82958000-82959200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr16:82958000-82959400	Enhancers	Psoas Muscle	Psoas
17	chr16:82958000-82959400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr16:82958000-82961000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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