Variant report

Variant	rs12459917
Chromosome Location	chr19:55686380-55686381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr19:55686332-55686842	K562	blood:	n/a	n/a
2	GTF2F1	chr19:55685898-55686782	K562	blood:	n/a	n/a
3	CCNT2	chr19:55686348-55686777	K562	blood:	n/a	n/a
4	NFYB	chr19:55686237-55686667	K562	blood:	n/a	chr19:55686464-55686479 chr19:55686464-55686479 chr19:55686467-55686477 chr19:55686468-55686480 chr19:55686465-55686479
5	POLR2A	chr19:55685563-55686879	K562	blood:	n/a	n/a
6	NRF1	chr19:55686358-55686730	H1-hESC	embryonic stem cell:	n/a	chr19:55686527-55686538 chr19:55686526-55686537 chr19:55686524-55686538
7	TBP	chr19:55685103-55686800	K562	blood:	n/a	n/a
8	E2F6	chr19:55686365-55687024	K562	blood:	n/a	chr19:55686468-55686477
9	RCOR1	chr19:55685301-55686528	K562	blood:	n/a	n/a
10	MAZ	chr19:55686319-55686793	K562	blood:	n/a	n/a
11	PML	chr19:55685067-55686889	K562	blood:	n/a	n/a
12	ZC3H11A	chr19:55685931-55686651	K562	blood:	n/a	n/a
13	POLR2A	chr19:55684921-55686855	K562	blood:	n/a	n/a
14	TAF1	chr19:55686319-55686711	K562	blood:	n/a	n/a
15	UBTF	chr19:55686191-55686793	K562	blood:	n/a	n/a
16	POLR2A	chr19:55684256-55687473	K562	blood:	n/a	n/a
17	POLR2A	chr19:55685838-55686769	H1-neurons	neurons:	n/a	n/a
18	JUN	chr19:55686338-55686808	K562	blood:	n/a	chr19:55686466-55686475
19	GTF2B	chr19:55686009-55686875	K562	blood:	n/a	n/a
20	POLR2A	chr19:55684725-55687295	K562	blood:	n/a	n/a
21	ELF1	chr19:55686361-55686801	K562	blood:	n/a	n/a
22	POLR2A	chr19:55685062-55686816	K562	blood:	n/a	n/a
23	MAX	chr19:55686342-55686987	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUN	chr19:55684455-55688134	K562	blood:	n/a	chr19:55686466-55686475 chr19:55687873-55687887 chr19:55685270-55685279
25	RCOR1	chr19:55686218-55686792	K562	blood:	n/a	n/a
26	POLR2A	chr19:55685070-55686963	K562	blood:	n/a	n/a
27	E2F6	chr19:55685634-55686994	H1-hESC	embryonic stem cell:	n/a	chr19:55686468-55686477
28	E2F4	chr19:55686380-55686790	K562	blood:	n/a	chr19:55686468-55686477 chr19:55686540-55686551 chr19:55686561-55686572
29	TAF1	chr19:55686378-55686794	K562	blood:	n/a	n/a
30	E2F6	chr19:55686309-55687003	H1-hESC	embryonic stem cell:	n/a	chr19:55686468-55686477
31	TEAD4	chr19:55685105-55686910	K562	blood:	n/a	n/a
32	EGR1	chr19:55686112-55686606	K562	blood:	n/a	chr19:55686528-55686537 chr19:55686486-55686496
33	ELF1	chr19:55686258-55686926	K562	blood:	n/a	n/a
34	EGR1	chr19:55686342-55686676	K562	blood:	n/a	chr19:55686528-55686537 chr19:55686486-55686496
35	POLR2A	chr19:55685890-55686864	K562	blood:	n/a	n/a
36	POLR2A	chr19:55685402-55688569	H1-neurons	neurons:	n/a	n/a
37	NRF1	chr19:55686379-55686697	K562	blood:	n/a	chr19:55686527-55686538 chr19:55686526-55686537 chr19:55686524-55686538
38	E2F6	chr19:55685609-55687141	K562	blood:	n/a	chr19:55686468-55686477
39	MAX	chr19:55685799-55687151	K562	blood:	n/a	n/a
40	HMGN3	chr19:55686370-55687171	K562	blood:	n/a	n/a
41	POLR2A	chr19:55685601-55686387	K562	blood:	n/a	n/a
42	POLR2A	chr19:55684911-55687042	K562	blood:	n/a	n/a
43	POLR2A	chr19:55684974-55686834	K562	blood:	n/a	n/a
44	IRF1	chr19:55686316-55686792	K562	blood:	n/a	chr19:55686503-55686517 chr19:55686485-55686499
45	HEY1	chr19:55685504-55686892	K562	blood:	n/a	n/a
46	NR2F2	chr19:55686213-55686926	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55683524..55688236-chr19:55723837..55729899,9	K562	blood:
2	chr19:55684227..55686502-chr19:56163659..56165514,2	K562	blood:
3	chr19:55685207..55686933-chr19:55998048..56001042,3	K562	blood:
4	chr19:55686310..55687891-chr19:55719950..55721494,2	K562	blood:
5	chr19:55684986..55687245-chr19:55917365..55919407,3	K562	blood:
6	chr19:55685793..55687332-chr19:56110126..56112536,2	K562	blood:
7	chr19:55652583..55654587-chr19:55685564..55687103,2	K562	blood:
8	chr19:55677803..55679380-chr19:55684043..55686956,2	MCF-7	breast:
9	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
10	chr19:55651262..55654083-chr19:55684163..55687103,3	K562	blood:
11	chr19:55682890..55686413-chr19:55726859..55729575,3	K562	blood:
12	chr19:55684707..55688022-chr19:55908129..55911789,4	K562	blood:
13	chr19:55590426..55594638-chr19:55684228..55687886,4	K562	blood:
14	chr19:55685149..55688070-chr19:55790255..55792658,4	K562	blood:
15	chr19:55624933..55628932-chr19:55685116..55688802,5	K562	blood:
16	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
17	chr19:55592011..55594638-chr19:55684282..55687431,3	K562	blood:
18	chr19:55685793..55687548-chr19:56110126..56112399,2	K562	blood:
19	chr19:55684986..55687548-chr19:55917710..55920086,4	K562	blood:
20	chr19:55627139..55630124-chr19:55683805..55687284,3	K562	blood:

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000125503	Chromatin interaction
ENSG00000179954	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000267110	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000105048	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]
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]
rs12460445	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]
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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55684400-55686800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:55684800-55686400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:55684800-55687000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:55684800-55687000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
5	chr19:55685000-55686400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
6	chr19:55685000-55686800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
7	chr19:55685200-55686800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:55685200-55690400	Weak transcription	Gastric	stomach
9	chr19:55685400-55687000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
10	chr19:55685400-55687000	Bivalent Enhancer	Placenta	Placenta
11	chr19:55685600-55686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:55685600-55686800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr19:55685600-55686800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr19:55685600-55687800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:55685600-55690400	Weak transcription	Pancreas	Pancrea
16	chr19:55685600-55690400	Weak transcription	Right Atrium	heart
17	chr19:55685800-55686400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
18	chr19:55685800-55686400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
19	chr19:55685800-55686800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:55685800-55686800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
21	chr19:55685800-55686800	Bivalent Enhancer	Spleen	Spleen
22	chr19:55685800-55687000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:55685800-55690200	Weak transcription	Osteobl	bone
24	chr19:55685800-55690400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:55686000-55686400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
26	chr19:55686000-55686400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:55686000-55686600	Active TSS	K562	blood
28	chr19:55686000-55686800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr19:55686000-55687000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:55686000-55687000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:55686000-55689200	Weak transcription	Hela-S3	cervix
32	chr19:55686000-55690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:55686000-55690200	Weak transcription	A549	lung
34	chr19:55686000-55690200	Weak transcription	NHEK	skin
35	chr19:55686200-55686400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
36	chr19:55686200-55686800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr19:55686200-55686800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:55686200-55687000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:55686200-55687200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:55686200-55688000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:55686200-55689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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