Variant report

Variant	rs6456876
Chromosome Location	chr6:28918936-28918937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28863784..28865629-chr6:28918637..28921778,3	MCF-7	breast:
2	chr6:28916396..28919032-chr6:28931395..28932899,2	K562	blood:
3	chr6:28918185..28920512-chr6:28921430..28924835,3	MCF-7	breast:
4	chr6:28889795..28892316-chr6:28916609..28919222,2	MCF-7	breast:
5	chr6:28918865..28920559-chr6:28953984..28955919,2	MCF-7	breast:
6	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
7	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
8	chr6:28916735..28919060-chr6:28983575..28986159,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1005123	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1237485	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1476016	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1543796	0.87[ASN][1000 genomes]
rs1794587	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs184093	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2013848	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2032500	0.88[ASN][1000 genomes]
rs2071785	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071790	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs209122	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs209126	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs209128	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs209129	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs209137	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209138	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs209148	0.89[ASN][1000 genomes]
rs209149	0.88[ASN][1000 genomes]
rs209152	0.82[ASN][1000 genomes]
rs209153	0.83[ASN][1000 genomes]
rs209160	0.83[ASN][1000 genomes]
rs209161	0.83[ASN][1000 genomes]
rs209163	0.83[ASN][1000 genomes]
rs209164	0.83[ASN][1000 genomes]
rs2157312	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2157313	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2179648	0.86[ASN][1000 genomes]
rs2187807	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187808	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269555	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2394512	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2765229	0.91[ASN][1000 genomes]
rs3129792	0.92[ASN][1000 genomes]
rs3129793	0.90[ASN][1000 genomes]
rs3130841	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3130842	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3130886	0.92[ASN][1000 genomes]
rs3130889	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3130897	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3131070	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3131074	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3131077	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3131100	0.82[ASN][1000 genomes]
rs3131102	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3135303	0.83[ASN][1000 genomes]
rs3135315	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3135319	0.80[ASN][1000 genomes]
rs3135321	0.92[ASN][1000 genomes]
rs3135322	0.92[ASN][1000 genomes]
rs3135323	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3135324	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3135326	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3135327	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3135328	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs381808	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs393431	0.83[ASN][1000 genomes]
rs4427026	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713186	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713187	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713188	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713190	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713192	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4947339	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456880	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6456883	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456891	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900967	0.80[ASN][1000 genomes]
rs6901599	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904975	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906909	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914955	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6916161	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6920392	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6931823	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763009	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7743189	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7755875	0.80[ASN][1000 genomes]
rs7761547	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7768299	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9257401	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257403	0.83[ASN][1000 genomes]
rs9257404	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9257405	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257408	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257421	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257447	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9257449	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9257455	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257461	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257464	0.85[EUR][1000 genomes]
rs9348816	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393939	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468467	0.86[ASN][1000 genomes]
rs9468472	0.83[EUR][1000 genomes];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6456876	ZNF323	cis	cerebellum	SCAN
rs6456876	ZSCAN16	cis	parietal	SCAN
rs6456876	HIST1H2AE	cis	parietal	SCAN
rs6456876	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28912200-28921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28912400-28920800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:28912400-28921200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:28912400-28921200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:28912400-28921200	Weak transcription	Right Atrium	heart
6	chr6:28915600-28921200	Weak transcription	Esophagus	oesophagus
7	chr6:28915800-28920600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:28916000-28920800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:28916000-28921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:28916200-28920800	Weak transcription	NH-A	brain
11	chr6:28916200-28920800	Weak transcription	Osteobl	bone
12	chr6:28916200-28921200	Weak transcription	HMEC	breast
13	chr6:28916200-28921200	Weak transcription	NHEK	skin
14	chr6:28916400-28921200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:28916600-28920600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:28916800-28921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:28917000-28919000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:28917000-28920800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:28917000-28921200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:28918200-28919800	Active TSS	Placenta	Placenta
21	chr6:28918400-28919200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:28918400-28919200	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr6:28918400-28919200	Flanking Active TSS	Hela-S3	cervix
24	chr6:28918400-28919200	Flanking Active TSS	K562	blood
25	chr6:28918400-28919600	Active TSS	A549	lung
26	chr6:28918600-28919000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:28918600-28919200	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr6:28918600-28921200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:28918800-28919200	Enhancers	HepG2	liver
30	chr6:28918800-28920800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:28918800-28920800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:28918800-28921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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