Variant report

Variant	rs386628
Chromosome Location	chr6:28784396-28784397
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	chr6:28767356..28769263-chr6:28782865..28784537,2	K562	blood:
2	chr6:28687325..28688855-chr6:28783516..28785419,2	K562	blood:
3	chr6:28187117..28189206-chr6:28783315..28785702,2	K562	blood:
4	chr6:28774872..28779186-chr6:28780865..28786550,9	K562	blood:
5	chr6:28722382..28724843-chr6:28784005..28786428,2	K562	blood:
6	chr6:28783316..28785641-chr6:28791797..28793442,2	K562	blood:
7	chr6:28688964..28691307-chr6:28783200..28785150,2	K562	blood:
8	chr6:28722382..28725655-chr6:28783034..28786428,3	K562	blood:

No data

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1002925	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233596	0.81[EUR][1000 genomes]
rs1233601	0.82[EUR][1000 genomes]
rs1233602	0.89[EUR][1000 genomes]
rs1233607	0.82[EUR][1000 genomes]
rs1233615	0.83[EUR][1000 genomes]
rs1233616	0.83[EUR][1000 genomes]
rs1233617	0.82[EUR][1000 genomes]
rs1235176	0.81[EUR][1000 genomes]
rs1237485	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1476016	0.87[EUR][1000 genomes]
rs169683	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1794587	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs184093	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2032500	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2071790	0.86[EUR][1000 genomes]
rs209122	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209126	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209128	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209129	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209137	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209138	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs209148	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209149	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs209152	0.91[EUR][1000 genomes]
rs209153	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209160	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs209161	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs209163	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs209164	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs209169	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs209171	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209173	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs209175	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs209176	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs209179	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209182	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs209184	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209186	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157312	0.84[EUR][1000 genomes]
rs2157313	0.86[EUR][1000 genomes]
rs2208536	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2754764	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2754767	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765218	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765219	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2765229	0.87[EUR][1000 genomes]
rs3129792	0.83[EUR][1000 genomes]
rs3129793	0.81[EUR][1000 genomes]
rs3130841	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130842	0.87[EUR][1000 genomes]
rs3130886	0.84[EUR][1000 genomes]
rs3130889	0.87[EUR][1000 genomes]
rs3130897	0.87[EUR][1000 genomes]
rs3131070	0.87[EUR][1000 genomes]
rs3131074	0.87[EUR][1000 genomes]
rs3131077	0.86[EUR][1000 genomes]
rs3131102	0.90[EUR][1000 genomes]
rs3131342	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3132371	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3132386	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3135303	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135315	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135321	0.83[EUR][1000 genomes]
rs3135322	0.85[EUR][1000 genomes]
rs3135323	0.86[EUR][1000 genomes]
rs3135324	0.86[EUR][1000 genomes]
rs3135326	0.80[EUR][1000 genomes]
rs3135327	0.83[EUR][1000 genomes]
rs3135328	0.86[EUR][1000 genomes]
rs377392	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381808	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs393431	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs526983	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6456857	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs763009	0.84[EUR][1000 genomes]
rs9257134	0.81[EUR][1000 genomes]
rs9257135	0.81[EUR][1000 genomes]
rs9257229	0.87[EUR][1000 genomes];0.82[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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv9558	chr6:28770281-28785058	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3410540	chr6:28770455-28785112	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3322630	chr6:28770519-28785092	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3486939	chr6:28770525-28785051	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3486940	chr6:28770525-28785051	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3403106	chr6:28770790-28785189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv970724	chr6:28778144-28784760	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs386628	ZNF323	cis	parietal	SCAN
rs386628	ZNF323	cis	cerebellum	SCAN
rs386628	ZSCAN23	cis	cerebellum	SCAN
rs386628	ZKSCAN3	cis	cerebellum	SCAN
rs386628	HIST1H2BH	cis	cerebellum	SCAN
rs386628	ZSCAN16	cis	parietal	SCAN
rs386628	NKAPL	cis	parietal	SCAN
rs386628	ZSCAN23	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28783600-28784800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:28784000-28784400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:28784000-28784400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:28784000-28784400	Bivalent Enhancer	HepG2	liver
5	chr6:28784000-28784400	Enhancers	HMEC	breast
6	chr6:28784000-28784600	Flanking Active TSS	K562	blood
7	chr6:28784000-28785000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
8	chr6:28784200-28784400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28784200-28784600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:28784200-28785400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:28784200-28786000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:28784200-28786200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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