Variant report

Variant	rs12460445
Chromosome Location	chr19:55686986-55686987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr19:55686893-55687169	K562	blood:	n/a	n/a
2	E2F6	chr19:55686365-55687024	K562	blood:	n/a	chr19:55686468-55686477
3	TBL1XR1	chr19:55686438-55687018	K562	blood:	n/a	n/a
4	MYC	chr19:55686429-55687022	K562	blood:	n/a	n/a
5	POLR2A	chr19:55684256-55687473	K562	blood:	n/a	n/a
6	POLR2A	chr19:55684725-55687295	K562	blood:	n/a	n/a
7	CBX3	chr19:55686424-55687129	K562	blood:	n/a	n/a
8	MAX	chr19:55686342-55686987	H1-hESC	embryonic stem cell:	n/a	n/a
9	JUN	chr19:55684455-55688134	K562	blood:	n/a	chr19:55686466-55686475 chr19:55687873-55687887 chr19:55685270-55685279
10	E2F6	chr19:55685634-55686994	H1-hESC	embryonic stem cell:	n/a	chr19:55686468-55686477
11	E2F6	chr19:55686309-55687003	H1-hESC	embryonic stem cell:	n/a	chr19:55686468-55686477
12	ELF1	chr19:55686829-55687139	K562	blood:	n/a	n/a
13	POLR2A	chr19:55685402-55688569	H1-neurons	neurons:	n/a	n/a
14	E2F6	chr19:55685609-55687141	K562	blood:	n/a	chr19:55686468-55686477
15	MAX	chr19:55685799-55687151	K562	blood:	n/a	n/a
16	SPI1	chr19:55686870-55687107	K562	blood:	n/a	chr19:55687028-55687041 chr19:55686995-55687008
17	HMGN3	chr19:55686370-55687171	K562	blood:	n/a	n/a
18	POLR2A	chr19:55684911-55687042	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55683524..55688236-chr19:55723837..55729899,9	K562	blood:
2	chr19:55686310..55687891-chr19:55719950..55721494,2	K562	blood:
3	chr19:55684986..55687245-chr19:55917365..55919407,3	K562	blood:
4	chr19:55685793..55687332-chr19:56110126..56112536,2	K562	blood:
5	chr19:55652583..55654587-chr19:55685564..55687103,2	K562	blood:
6	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
7	chr19:55651262..55654083-chr19:55684163..55687103,3	K562	blood:
8	chr19:55684707..55688022-chr19:55908129..55911789,4	K562	blood:
9	chr19:55590426..55594638-chr19:55684228..55687886,4	K562	blood:
10	chr19:55685149..55688070-chr19:55790255..55792658,4	K562	blood:
11	chr19:55624933..55628932-chr19:55685116..55688802,5	K562	blood:
12	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
13	chr19:55592011..55594638-chr19:55684282..55687431,3	K562	blood:
14	chr19:55685793..55687548-chr19:56110126..56112399,2	K562	blood:
15	chr19:55684986..55687548-chr19:55917710..55920086,4	K562	blood:
16	chr19:55627139..55630124-chr19:55683805..55687284,3	K562	blood:

No data

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000129990	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000267649	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10423713	0.80[ASN][1000 genomes]
rs1128712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459930	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461148	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462430	0.83[MEX][hapmap]
rs12463268	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17458	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2071572	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278281	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288420	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288518	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2288528	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288529	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745922	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3786867	0.94[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3803903	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3826887	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3848618	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3859544	0.94[ASN][1000 genomes]
rs56666700	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56726774	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58017412	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58218194	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58824375	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59663064	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60176657	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60799292	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61570139	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61704307	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7247152	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7247378	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7248997	0.94[JPT][hapmap]
rs7255625	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs8101500	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs890871	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9710458	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55684800-55687000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr19:55684800-55687000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
3	chr19:55685200-55690400	Weak transcription	Gastric	stomach
4	chr19:55685400-55687000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
5	chr19:55685400-55687000	Bivalent Enhancer	Placenta	Placenta
6	chr19:55685600-55687800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr19:55685600-55690400	Weak transcription	Pancreas	Pancrea
8	chr19:55685600-55690400	Weak transcription	Right Atrium	heart
9	chr19:55685800-55687000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:55685800-55690200	Weak transcription	Osteobl	bone
11	chr19:55685800-55690400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:55686000-55687000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:55686000-55687000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:55686000-55689200	Weak transcription	Hela-S3	cervix
15	chr19:55686000-55690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:55686000-55690200	Weak transcription	A549	lung
17	chr19:55686000-55690200	Weak transcription	NHEK	skin
18	chr19:55686200-55687000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:55686200-55687200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:55686200-55688000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:55686200-55689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:55686600-55687000	Bivalent Enhancer	Fetal Thymus	thymus
23	chr19:55686600-55687400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:55686600-55687800	Flanking Active TSS	K562	blood
25	chr19:55686800-55687000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:55686800-55687400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
27	chr19:55686800-55688000	Enhancers	H9 Cell Line	embryonic stem cell
28	chr19:55686800-55688200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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