Variant report

Variant	rs1476016
Chromosome Location	chr6:28922719-28922720
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28804076..28806200-chr6:28922392..28924838,2	K562	blood:
2	chr6:28922600..28925578-chr6:28943937..28946823,4	K562	blood:
3	chr6:28921551..28923708-chr6:28958891..28962206,3	K562	blood:
4	chr6:28863289..28866205-chr6:28921133..28924025,2	K562	blood:
5	chr6:28920218..28924369-chr6:28968578..28972504,4	K562	blood:
6	chr6:28920183..28922796-chr6:28965172..28967810,2	K562	blood:
7	chr22:29197206..29200027-chr6:28920726..28923051,2	MCF-7	breast:
8	chr6:28907315..28909915-chr6:28920300..28923261,2	MCF-7	breast:
9	chr6:28889277..28892149-chr6:28920165..28923545,3	K562	blood:
10	chr6:28918185..28920512-chr6:28921430..28924835,3	MCF-7	breast:
11	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
12	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
13	chr6:28676149..28677937-chr6:28921476..28924088,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1002925	0.89[EUR][1000 genomes]
rs1005123	0.90[ASN][1000 genomes]
rs1237485	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543796	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs169683	0.86[EUR][1000 genomes]
rs1794587	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs184093	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2006173	0.81[EUR][1000 genomes]
rs2013848	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2032500	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2071785	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2071790	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209122	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209126	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs209128	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209129	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209137	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209138	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209148	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209149	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs209152	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs209153	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs209160	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs209161	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs209163	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs209164	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs209169	0.80[EUR][1000 genomes]
rs209171	0.85[EUR][1000 genomes]
rs209173	0.86[EUR][1000 genomes]
rs209175	0.85[EUR][1000 genomes]
rs209176	0.89[EUR][1000 genomes]
rs209179	0.86[EUR][1000 genomes]
rs209184	0.87[EUR][1000 genomes]
rs209186	0.86[EUR][1000 genomes]
rs2157312	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2157313	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179648	0.87[ASN][1000 genomes]
rs2187807	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2187808	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2208536	0.86[EUR][1000 genomes]
rs2269555	0.90[ASN][1000 genomes]
rs2394512	0.88[ASN][1000 genomes]
rs2754764	0.86[EUR][1000 genomes]
rs2754767	0.86[EUR][1000 genomes]
rs2765218	0.85[EUR][1000 genomes]
rs2765219	0.86[EUR][1000 genomes]
rs2765229	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129792	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3129793	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130841	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130842	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130886	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130889	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130897	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3131070	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3131074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131077	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131100	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3131102	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131342	0.86[EUR][1000 genomes]
rs3132371	0.82[EUR][1000 genomes]
rs3132386	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3135303	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135315	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3135319	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135321	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135322	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3135323	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3135324	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3135326	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3135327	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135328	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs377392	0.87[EUR][1000 genomes]
rs381808	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs386628	0.87[EUR][1000 genomes]
rs393431	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4427026	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713186	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4713187	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4713188	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4713190	0.92[ASN][1000 genomes]
rs4713192	0.92[ASN][1000 genomes]
rs4947339	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs526983	0.86[EUR][1000 genomes]
rs6456876	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6456880	0.92[ASN][1000 genomes]
rs6456883	0.90[ASN][1000 genomes]
rs6456891	0.85[ASN][1000 genomes]
rs6900967	0.81[ASN][1000 genomes]
rs6901599	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6904975	0.91[ASN][1000 genomes]
rs6906909	0.91[ASN][1000 genomes]
rs6914955	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6916161	0.90[ASN][1000 genomes]
rs6920392	0.92[ASN][1000 genomes]
rs6931823	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs763009	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743189	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7761547	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7768299	0.88[ASN][1000 genomes]
rs9257401	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9257403	0.85[ASN][1000 genomes]
rs9257404	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9257405	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9257408	0.88[ASN][1000 genomes]
rs9257421	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9257447	0.92[ASN][1000 genomes]
rs9257449	0.92[ASN][1000 genomes]
rs9257455	0.89[ASN][1000 genomes]
rs9257461	0.90[ASN][1000 genomes]
rs9348816	0.88[ASN][1000 genomes]
rs9393939	0.88[ASN][1000 genomes]
rs9468467	0.87[ASN][1000 genomes]
rs9468472	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1476016	ZKSCAN3	cis	cerebellum	SCAN
rs1476016	ZNF323	cis	parietal	SCAN
rs1476016	NKAPL	cis	parietal	SCAN
rs1476016	HIST1H2BH	cis	cerebellum	SCAN
rs1476016	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28921000-28922800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:28921200-28922800	Active TSS	Colonic Mucosa	Colon
3	chr6:28921600-28922800	Active TSS	Fetal Intestine Small	intestine
4	chr6:28922000-28923200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:28922000-28923400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:28922200-28922800	Active TSS	Duodenum Mucosa	Duodenum
7	chr6:28922200-28923000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:28922200-28923000	Enhancers	K562	blood
9	chr6:28922200-28923200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:28922200-28923800	Enhancers	NHEK	skin
11	chr6:28922200-28928400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:28922200-28930600	Weak transcription	Right Atrium	heart
13	chr6:28922400-28922800	Active TSS	Fetal Intestine Large	intestine
14	chr6:28922600-28923000	Flanking Active TSS	HepG2	liver
15	chr6:28922600-28923200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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