Variant report

Variant	rs9319579
Chromosome Location	chr16:82958442-82958443
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	TCF7L2	chr16:82957385-82958697	HEK293	kidney:	n/a	chr16:82957827-82957843 chr16:82957827-82957843 chr16:82957829-82957839 chr16:82957831-82957840 chr16:82957828-82957842
2	KAP1	chr16:82957989-82958511	HEK293	kidney:	n/a	n/a
3	KAP1	chr16:82958092-82958672	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
CDH13	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1008648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150522	0.84[ASN][1000 genomes]
rs11150523	0.88[ASN][1000 genomes]
rs12102479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[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];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011241	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216734	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216735	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2216736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2325691	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417188	0.88[ASN][1000 genomes]
rs28457841	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661446	0.88[ASN][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];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273031	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312297	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4485359	1.00[ASN][1000 genomes]
rs4569269	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4584813	0.96[ASN][1000 genomes]
rs4616278	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635337	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4782737	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4782738	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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	0.84[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];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7404959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7501309	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046347	0.89[ASN][1000 genomes]
rs8050643	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]
rs8050659	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];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923309	0.86[ASN][1000 genomes]
rs9926654	0.88[ASN][1000 genomes]
rs9928115	0.82[AMR][1000 genomes];0.81[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];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941054	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[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
rs9319579	USP10	cis	cerebellum	SCAN
rs9319579	COTL1	cis	parietal	SCAN

Chromatin state (count:24 , 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	chr16:82957400-82959200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr16:82957800-82959600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr16:82957800-82959600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr16:82957800-82960200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr16:82958000-82959200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr16:82958000-82959400	Enhancers	Psoas Muscle	Psoas
14	chr16:82958000-82959400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr16:82958000-82961000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr16:82958200-82959200	Enhancers	Fetal Heart	heart
17	chr16:82958200-82959400	Enhancers	Right Ventricle	heart
18	chr16:82958200-82959400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr16:82958200-82960800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr16:82958400-82959000	Bivalent Enhancer	Primary T cells from cord blood	blood
21	chr16:82958400-82959000	Weak transcription	Right Atrium	heart
22	chr16:82958400-82959400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr16:82958400-82959600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr16:82958400-82966000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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