Variant report

Variant	rs763009
Chromosome Location	chr6:28915108-28915109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28915108..28916611-chr6:28956143..28957725,2	K562	blood:
2	chr6:28908842..28913919-chr6:28914065..28917198,6	K562	blood:
3	chr6:28889181..28892324-chr6:28914059..28916550,3	MCF-7	breast:
4	chr6:28914281..28916611-chr6:28956056..28957643,2	K562	blood:
5	chr6:28830059..28832659-chr6:28914620..28916802,2	K562	blood:
6	chr6:28913503..28915110-chr6:28972198..28974208,2	MCF-7	breast:
7	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:

Variant related genes	Relation type
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000263426	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1002925	0.86[EUR][1000 genomes]
rs1005123	0.88[ASN][1000 genomes]
rs1237485	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1476016	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1543796	0.87[ASN][1000 genomes]
rs169683	0.83[EUR][1000 genomes]
rs1794587	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs184093	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2013848	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2032500	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071785	0.95[ASN][1000 genomes]
rs2071790	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs209122	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209126	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209128	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209129	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209137	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs209138	0.89[EUR][1000 genomes]
rs209148	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209149	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209152	0.85[EUR][1000 genomes]
rs209153	0.88[EUR][1000 genomes]
rs209160	0.90[EUR][1000 genomes]
rs209161	0.88[EUR][1000 genomes]
rs209163	0.88[EUR][1000 genomes]
rs209164	0.85[EUR][1000 genomes]
rs209171	0.82[EUR][1000 genomes]
rs209173	0.83[EUR][1000 genomes]
rs209175	0.82[EUR][1000 genomes]
rs209176	0.86[EUR][1000 genomes]
rs209179	0.83[EUR][1000 genomes]
rs209182	0.81[EUR][1000 genomes]
rs209184	0.84[EUR][1000 genomes]
rs209186	0.83[EUR][1000 genomes]
rs2157312	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2157313	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2179648	0.85[ASN][1000 genomes]
rs2187807	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2187808	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2208536	0.83[EUR][1000 genomes]
rs2269555	0.89[ASN][1000 genomes]
rs2394512	0.87[ASN][1000 genomes]
rs2754764	0.83[EUR][1000 genomes]
rs2754767	0.83[EUR][1000 genomes]
rs2765218	0.82[EUR][1000 genomes]
rs2765219	0.83[EUR][1000 genomes]
rs2765229	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3129792	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3129793	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130841	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130842	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130886	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130889	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3130897	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3131070	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131074	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3131077	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3131100	0.81[EUR][1000 genomes]
rs3131102	0.92[EUR][1000 genomes]
rs3131342	0.83[EUR][1000 genomes]
rs3132386	0.86[EUR][1000 genomes]
rs3135303	0.88[EUR][1000 genomes]
rs3135315	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135319	0.83[EUR][1000 genomes]
rs3135321	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3135322	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3135323	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3135324	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3135326	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3135327	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3135328	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs377392	0.84[EUR][1000 genomes]
rs381808	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs386628	0.84[EUR][1000 genomes]
rs393431	0.86[EUR][1000 genomes]
rs4427026	0.98[ASN][1000 genomes]
rs4713186	0.93[ASN][1000 genomes]
rs4713187	0.93[ASN][1000 genomes]
rs4713188	0.95[ASN][1000 genomes]
rs4713190	0.91[ASN][1000 genomes]
rs4713192	0.91[ASN][1000 genomes]
rs4947339	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs526983	0.83[EUR][1000 genomes]
rs6456876	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6456880	0.90[ASN][1000 genomes]
rs6456883	0.89[ASN][1000 genomes]
rs6456891	0.83[ASN][1000 genomes]
rs6901599	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6904975	0.90[ASN][1000 genomes]
rs6906909	0.90[ASN][1000 genomes]
rs6914955	0.95[ASN][1000 genomes]
rs6916161	0.89[ASN][1000 genomes]
rs6920392	0.91[ASN][1000 genomes]
rs6931823	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7743189	0.97[ASN][1000 genomes]
rs7761547	0.98[ASN][1000 genomes]
rs7768299	0.87[ASN][1000 genomes]
rs9257401	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9257403	0.83[ASN][1000 genomes]
rs9257404	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9257405	0.95[ASN][1000 genomes]
rs9257408	0.87[ASN][1000 genomes]
rs9257421	0.95[ASN][1000 genomes]
rs9257447	0.90[ASN][1000 genomes]
rs9257449	0.90[ASN][1000 genomes]
rs9257455	0.87[ASN][1000 genomes]
rs9257461	0.89[ASN][1000 genomes]
rs9348816	0.87[ASN][1000 genomes]
rs9393939	0.87[ASN][1000 genomes]
rs9468467	0.85[ASN][1000 genomes]
rs9468472	0.83[ASN][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	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs763009	ZSCAN16	cis	parietal	SCAN
rs763009	NKAPL	cis	parietal	SCAN
rs763009	ZSCAN23	cis	parietal	SCAN
rs763009	ZKSCAN3	cis	cerebellum	SCAN
rs763009	ZSCAN23	cis	cerebellum	SCAN
rs763009	HIST1H2BH	cis	cerebellum	SCAN
rs763009	ZNF323	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28912200-28915200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:28912200-28915600	Weak transcription	Pancreas	Pancrea
3	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:28912400-28915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:28912400-28915200	Weak transcription	Colonic Mucosa	Colon
6	chr6:28912400-28915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:28912400-28915400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:28912400-28915400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28912400-28915400	Weak transcription	Esophagus	oesophagus
10	chr6:28912400-28915400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:28912400-28915400	Weak transcription	A549	lung
12	chr6:28912400-28915400	Weak transcription	HUVEC	blood vessel
13	chr6:28912400-28915400	Weak transcription	NHEK	skin
14	chr6:28912400-28915600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:28912400-28915600	Weak transcription	HMEC	breast
16	chr6:28912400-28915800	Weak transcription	NH-A	brain
17	chr6:28912400-28915800	Weak transcription	Osteobl	bone
18	chr6:28912400-28916000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:28912400-28916200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:28912400-28916800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:28912400-28920800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
24	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
25	chr6:28912600-28915400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:28912600-28915400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:28912800-28915400	Enhancers	HepG2	liver
28	chr6:28912800-28915600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:28912800-28915800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:28912800-28916000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:28913200-28916600	Enhancers	K562	blood
32	chr6:28913400-28915400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:28914400-28917000	Enhancers	Hela-S3	cervix
34	chr6:28914800-28915800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:28915000-28915400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:28915000-28915800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:28915000-28916200	Enhancers	Stomach Mucosa	stomach

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