Variant report

Variant	rs6456880
Chromosome Location	chr6:28963248-28963249
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28960728..28968463-chr6:28970542..28974466,8	MCF-7	breast:
2	chr6:28687492..28689983-chr6:28961733..28963921,2	K562	blood:
3	chr6:28891221..28893414-chr6:28961724..28964196,2	K562	blood:
4	chr6:28948706..28953416-chr6:28959003..28967079,12	K562	blood:

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000197935	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1005123	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1237485	0.86[ASN][1000 genomes]
rs1476016	0.92[ASN][1000 genomes]
rs1543796	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1794587	0.84[ASN][1000 genomes]
rs184093	0.85[ASN][1000 genomes]
rs2013848	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2032500	0.83[ASN][1000 genomes]
rs2071785	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071790	0.89[ASN][1000 genomes]
rs209122	0.86[ASN][1000 genomes]
rs209126	0.86[ASN][1000 genomes]
rs209128	0.85[ASN][1000 genomes]
rs209129	0.85[ASN][1000 genomes]
rs209137	0.83[ASN][1000 genomes]
rs209148	0.84[ASN][1000 genomes]
rs209149	0.82[ASN][1000 genomes]
rs2157312	0.91[ASN][1000 genomes]
rs2157313	0.91[ASN][1000 genomes]
rs2179648	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2187807	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187808	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2269555	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394512	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2765229	0.85[ASN][1000 genomes]
rs3129097	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3129792	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3129793	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3130775	0.81[AMR][1000 genomes]
rs3130841	0.86[ASN][1000 genomes]
rs3130842	0.90[ASN][1000 genomes]
rs3130886	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3130889	0.91[ASN][1000 genomes]
rs3130897	0.89[ASN][1000 genomes]
rs3131070	0.90[ASN][1000 genomes]
rs3131074	0.91[ASN][1000 genomes]
rs3131077	0.91[ASN][1000 genomes]
rs3135319	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3135321	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3135322	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3135323	0.92[ASN][1000 genomes]
rs3135324	0.92[ASN][1000 genomes]
rs3135326	0.80[ASN][1000 genomes]
rs3135327	0.83[ASN][1000 genomes]
rs3135328	0.88[ASN][1000 genomes]
rs381808	0.84[ASN][1000 genomes]
rs4427026	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713186	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713187	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713188	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713190	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713192	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947339	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6456876	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6456883	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456891	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6900967	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6901599	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6904975	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906909	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914955	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916161	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920392	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927132	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6931823	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs763009	0.90[ASN][1000 genomes]
rs7743189	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7761547	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7768299	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9257401	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257404	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257405	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257408	0.82[ASN][1000 genomes]
rs9257421	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257447	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257449	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257455	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9257461	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9257464	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9348816	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348817	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9380109	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9393939	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393942	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9468467	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468472	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468480	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv1023028	chr6:28956136-29343575	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv538170	chr6:28956136-29343575	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6456880	ZKSCAN3	cis	cerebellum	SCAN
rs6456880	ZNF323	cis	cerebellum	SCAN
rs6456880	HIST1H2AE	cis	parietal	SCAN
rs6456880	ZSCAN16	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28957200-28972600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr6:28958400-28972800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:28959400-28972600	Weak transcription	Brain Germinal Matrix	brain
4	chr6:28962400-28964000	ZNF genes & repeats	K562	blood
5	chr6:28962400-28967200	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:28962600-28963800	Strong transcription	Fetal Brain Female	brain
7	chr6:28962600-28973000	Weak transcription	Left Ventricle	heart
8	chr6:28962800-28963600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
9	chr6:28962800-28965200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:28962800-28972600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:28963000-28963800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:28963000-28963800	ZNF genes & repeats	Adipose Nuclei	Adipose
13	chr6:28963000-28963800	ZNF genes & repeats	Aorta	Aorta
14	chr6:28963000-28963800	ZNF genes & repeats	Gastric	stomach
15	chr6:28963000-28964000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:28963000-28964000	Strong transcription	Brain Anterior Caudate	brain
17	chr6:28963000-28964200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr6:28963200-28963400	ZNF genes & repeats	Fetal Lung	lung
19	chr6:28963200-28963600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
20	chr6:28963200-28963600	ZNF genes & repeats	Pancreas	Pancrea
21	chr6:28963200-28963800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:28963200-28963800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:28963200-28963800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:28963200-28963800	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr6:28963200-28964000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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