Variant report

Variant	rs9930233
Chromosome Location	chr16:82881094-82881095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:82874724..82877200-chr16:82880596..82882100,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221395	Chromatin interaction

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

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

rs_ID	r²[population]
rs1008648	1.00[CHB][hapmap]
rs10492859	1.00[CHD][hapmap]
rs10871437	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11150494	0.81[EUR][1000 genomes]
rs11150495	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11150522	1.00[JPT][hapmap]
rs11640449	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12102479	1.00[CHB][hapmap]
rs12148992	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12923557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1381504	1.00[CHD][hapmap]
rs16958850	1.00[JPT][hapmap]
rs16958852	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16958858	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17673003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17674527	1.00[JPT][hapmap]
rs17675094	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17743051	1.00[CHB][hapmap]
rs1991028	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2011228	1.00[CHB][hapmap]
rs2216736	1.00[CHB][hapmap]
rs28433236	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28435993	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28701624	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3848298	1.00[CHB][hapmap]
rs4273030	1.00[CHB][hapmap]
rs4273031	1.00[CHB][hapmap]
rs4312297	1.00[CHB][hapmap]
rs4782737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4783300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6565078	1.00[JPT][hapmap]
rs7190538	1.00[JPT][hapmap]
rs725514	1.00[CHD][hapmap]
rs72807823	0.91[AMR][1000 genomes]
rs72807825	0.86[AMR][1000 genomes]
rs72807836	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7404932	1.00[CHB][hapmap]
rs7404959	1.00[CHB][hapmap]
rs7405300	1.00[CHB][hapmap]
rs7501309	1.00[CHB][hapmap]
rs8050643	1.00[CHB][hapmap]
rs8050659	1.00[CHB][hapmap]
rs8052619	1.00[CHB][hapmap]
rs918658	0.81[CEU][hapmap]
rs9319575	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9319579	1.00[CHB][hapmap]
rs9933074	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9933346	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9933458	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9933518	0.89[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs9935254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9936335	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9936407	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9938031	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9939413	1.00[CHD][hapmap]
rs9940251	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs9941054	1.00[CHB][hapmap]
rs9941327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs995506	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv573379	chr16:82713551-82887631	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	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
7	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
rs9930233	CDH13	cis	parietal	SCAN
rs9930233	COTL1	cis	parietal	SCAN

Chromatin state (count:16 , 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	chr16:82863200-82892800	Weak transcription	HSMMtube	muscle
3	chr16:82876800-82892400	Weak transcription	HSMM	muscle
4	chr16:82877000-82881400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr16:82879200-82886000	Weak transcription	Right Ventricle	heart
6	chr16:82879200-82907000	Weak transcription	Left Ventricle	heart
7	chr16:82879400-82891400	Weak transcription	Fetal Muscle Leg	muscle
8	chr16:82880400-82881400	Enhancers	HMEC	breast
9	chr16:82880800-82881400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr16:82880800-82881400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr16:82880800-82881400	Enhancers	Aorta	Aorta
12	chr16:82880800-82889200	Weak transcription	Psoas Muscle	Psoas
13	chr16:82880800-82892000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:82880800-82892000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr16:82880800-82893200	Weak transcription	NHEK	skin
16	chr16:82881000-82882800	Enhancers	Fetal Heart	heart

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