Variant report

Variant	rs9934789
Chromosome Location	chr16:71662467-71662468
allele	A/G
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	ZNF263	chr16:71661781-71662493	HEK293-T-REx	kidney:	n/a	chr16:71661883-71661892

No.	Distal block	Cell Line	Cell type
1	chr16:71658952..71666464-chr16:71755738..71760832,8	MCF-7	breast:
2	chr16:71660779..71663588-chr16:71917487..71919954,2	MCF-7	breast:
3	chr16:71597451..71600395-chr16:71660172..71663639,3	MCF-7	breast:

Variant related genes	Relation type
MARVELD3	TF binding region
ENSG00000260593	TF binding region
ENSG00000261513	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000260886	Chromatin interaction
ENSG00000157429	Chromatin interaction
ENSG00000040199	Chromatin interaction
ENSG00000102984	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1058750	0.88[EUR][1000 genomes]
rs10852502	0.90[EUR][1000 genomes]
rs10852503	0.89[EUR][1000 genomes]
rs11075893	0.86[EUR][1000 genomes]
rs11075894	0.86[EUR][1000 genomes]
rs11075898	0.85[EUR][1000 genomes]
rs11862723	0.85[EUR][1000 genomes]
rs1423983	0.86[EUR][1000 genomes]
rs2032918	0.85[EUR][1000 genomes]
rs2052584	0.86[EUR][1000 genomes]
rs2052585	0.89[EUR][1000 genomes]
rs2334880	0.89[EUR][1000 genomes]
rs4354946	0.88[EUR][1000 genomes]
rs4788548	0.87[EUR][1000 genomes]
rs4788550	0.86[EUR][1000 genomes]
rs4788820	0.86[EUR][1000 genomes]
rs4788822	0.88[EUR][1000 genomes]
rs4788823	0.88[EUR][1000 genomes]
rs4788825	0.84[EUR][1000 genomes]
rs4788828	0.86[EUR][1000 genomes]
rs4788830	0.86[EUR][1000 genomes]
rs6499526	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6499527	0.88[EUR][1000 genomes]
rs6499528	0.88[EUR][1000 genomes]
rs6499529	0.85[EUR][1000 genomes]
rs6499530	0.86[EUR][1000 genomes]
rs6499531	0.83[EUR][1000 genomes]
rs6499534	0.82[EUR][1000 genomes]
rs6499538	0.81[EUR][1000 genomes]
rs7187948	0.84[EUR][1000 genomes]
rs7188675	0.88[EUR][1000 genomes]
rs7190487	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7193549	0.88[EUR][1000 genomes]
rs7195059	0.86[EUR][1000 genomes]
rs7202479	0.81[EUR][1000 genomes]
rs7204608	0.88[EUR][1000 genomes]
rs7204992	0.89[EUR][1000 genomes]
rs7206470	0.89[EUR][1000 genomes]
rs8053745	0.86[EUR][1000 genomes]
rs8058297	0.89[EUR][1000 genomes]
rs8062188	0.86[EUR][1000 genomes]
rs979790	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9888756	0.81[EUR][1000 genomes]
rs9931074	0.86[EUR][1000 genomes]
rs9934301	0.82[EUR][1000 genomes]
rs9939458	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9934789	MARVELD3	cis	Skin Sun Exposed Lower leg	GTEx
rs9934789	PHLPP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71659600-71662800	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr16:71661000-71662600	Active TSS	Colonic Mucosa	Colon
3	chr16:71661000-71662600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:71661000-71662600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr16:71661000-71671000	Weak transcription	Right Atrium	heart
6	chr16:71661000-71674200	Weak transcription	Gastric	stomach
7	chr16:71661200-71662600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr16:71661200-71662800	Weak transcription	Liver	Liver
9	chr16:71661200-71662800	Weak transcription	HMEC	breast
10	chr16:71661200-71663200	Weak transcription	Esophagus	oesophagus
11	chr16:71661200-71663800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr16:71661200-71664000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr16:71661200-71667000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr16:71661400-71662800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr16:71661600-71663000	Weak transcription	HepG2	liver
16	chr16:71661600-71663400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:71661800-71662600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr16:71661800-71662600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
19	chr16:71661800-71662600	Enhancers	Ovary	ovary
20	chr16:71661800-71682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr16:71662000-71662600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr16:71662000-71662600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr16:71662000-71662800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr16:71662000-71662800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr16:71662000-71662800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr16:71662000-71662800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr16:71662000-71663000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr16:71662000-71663000	Weak transcription	HSMMtube	muscle
29	chr16:71662000-71663800	Enhancers	Pancreas	Pancrea
30	chr16:71662000-71674200	Weak transcription	Lung	lung
31	chr16:71662200-71663200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr16:71662200-71665600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr16:71662200-71671200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr16:71662400-71662600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr16:71662400-71663000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
36	chr16:71662400-71663400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr16:71662400-71663400	Genic enhancers	Duodenum Mucosa	Duodenum
38	chr16:71662400-71663400	Genic enhancers	Fetal Intestine Small	intestine
39	chr16:71662400-71663800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr16:71662400-71664000	Enhancers	NHEK	skin

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