Variant report

Variant	rs12459704
Chromosome Location	chr19:36707022-36707023
allele	C/T
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	REST	chr19:36704763-36707048	H1-neurons	neurons:	n/a	chr19:36705953-36705966 chr19:36705449-36705459 chr19:36705169-36705178
2	POLR2A	chr19:36704892-36707104	PFSK-1	brain:	n/a	n/a
3	MXI1	chr19:36704643-36707239	SK-N-SH	brain:	n/a	chr19:36706077-36706086
4	POLR2A	chr19:36706592-36707039	K562	blood:	n/a	n/a
5	TBL1XR1	chr19:36706448-36707107	K562	blood:	n/a	n/a
6	POLR2A	chr19:36704904-36707081	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:36705012-36708000	PANC-1	pancreas:	n/a	n/a
8	SP1	chr19:36704766-36707089	A549	lung:	n/a	chr19:36705832-36705844 chr19:36705496-36705509 chr19:36705494-36705506 chr19:36706940-36706950 chr19:36705496-36705505 chr19:36706940-36706949 chr19:36705495-36705504 chr19:36706940-36706950 chr19:36706939-36706951 chr19:36706941-36706950 chr19:36705829-36705843 chr19:36705833-36705842 chr19:36706940-36706949 chr19:36705494-36705506 chr19:36706939-36706951
9	POLR2A	chr19:36704947-36707096	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:36705217-36707065	MCF10A-Er-Src	breast:	n/a	n/a
11	KAP1	chr19:36704911-36707082	U2OS	brain:	n/a	n/a
12	EGR1	chr19:36706805-36707041	K562	blood:	n/a	chr19:36706943-36706953 chr19:36706943-36706952 chr19:36706942-36706955 chr19:36706942-36706955 chr19:36706942-36706952 chr19:36706942-36706955 chr19:36706941-36706955 chr19:36706942-36706955
13	POLR2A	chr19:36705901-36707073	K562	blood:	n/a	n/a
14	ETS1	chr19:36704722-36707071	A549	lung:	n/a	chr19:36705617-36705630 chr19:36706941-36706952 chr19:36706387-36706400 chr19:36705618-36705631 chr19:36705875-36705888 chr19:36705831-36705842
15	REST	chr19:36704653-36707128	A549	lung:	n/a	chr19:36705953-36705966 chr19:36705449-36705459 chr19:36705169-36705178
16	POLR2A	chr19:36706617-36707041	HUVEC	blood vessel:	n/a	n/a
17	MYC	chr19:36704793-36707082	MCF10A-Er-Src	breast:	n/a	n/a
18	MYC	chr19:36704495-36707047	A549	lung:	n/a	n/a
19	POLR2A	chr19:36704595-36707076	GM12892	blood:	n/a	n/a
20	IRF1	chr19:36705227-36707081	K562	blood:	n/a	chr19:36705492-36705506 chr19:36706500-36706516 chr19:36706304-36706318
21	CHD1	chr19:36704580-36707460	IMR90	lung:	n/a	chr19:36706939-36706949 chr19:36705832-36705842
22	POLR2A	chr19:36704993-36707037	SK-N-MC	brain:	n/a	n/a
23	MAX	chr19:36704602-36707096	A549	lung:	n/a	n/a
24	MXI1	chr19:36705146-36707143	K562	blood:	n/a	chr19:36706077-36706086
25	EGR1	chr19:36706680-36707049	K562	blood:	n/a	chr19:36706943-36706953 chr19:36706943-36706952 chr19:36706942-36706955 chr19:36706942-36706955 chr19:36706942-36706952 chr19:36706942-36706955 chr19:36706941-36706955 chr19:36706942-36706955
26	POLR2A	chr19:36705100-36707178	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr19:36704767-36707348	IMR90	lung:	n/a	n/a
28	POLR2A	chr19:36706659-36707066	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr19:36704740-36707036	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:36704685-36707044	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr19:36706565-36707025	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36679317..36682281-chr19:36704526..36707611,3	MCF-7	breast:
2	chr19:36705785..36707917-chr19:36719166..36721745,2	K562	blood:
3	chr19:36704317..36708058-chr19:36719298..36721271,3	MCF-7	breast:
4	chr19:36630466..36632159-chr19:36704253..36707369,3	K562	blood:
5	chr19:36630738..36632299-chr19:36705733..36707758,2	MCF-7	breast:
6	chr19:36706883..36709067-chr19:36978381..36980309,2	K562	blood:
7	chr19:36706964..36709175-chr20:49993312..49995838,2	MCF-7	breast:
8	chr19:36629887..36633258-chr19:36704150..36708473,10	K562	blood:
9	chr19:36705027..36707515-chr19:37176765..37178367,2	MCF-7	breast:
10	chr19:36635772..36637555-chr19:36705789..36707718,2	K562	blood:

Variant related genes	Relation type
ZNF565	TF binding region
ENSG00000167635	Chromatin interaction
ENSG00000263645	Chromatin interaction
ENSG00000225975	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000264276	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10403738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10407835	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407850	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409983	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412832	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415410	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416742	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419269	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425166	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882933	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12460466	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461077	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461112	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461855	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462725	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs17206379	0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs2271842	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs28414272	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528757	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857	0.82[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs2945955	0.90[CHB][hapmap]
rs2945989	0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs3098393	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs4361039	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806293	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806294	0.91[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806295	0.81[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56206115	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56316708	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56686317	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57385903	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57734651	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59026641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59295196	0.96[ASN][1000 genomes]
rs61413061	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113093	0.90[EUR][1000 genomes]
rs62113146	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113148	0.83[ASN][1000 genomes]
rs7251745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038028	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73040107	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73040113	0.84[ASN][1000 genomes]
rs8106135	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12459704	ZFP14	cis	lymphoblastoid	seeQTL
rs12459704	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs12459704	ZNF527	cis	cerebellum	SCAN
rs12459704	ZNF781	cis	cerebellum	SCAN
rs12459704	ZNF222	cis	parietal	SCAN
rs12459704	MEGF8	cis	cerebellum	SCAN
rs12459704	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs12459704	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36704000-36707400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:36704600-36707200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:36704600-36707200	Active TSS	NH-A	brain
4	chr19:36704600-36707400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:36704600-36707400	Active TSS	A549	lung
6	chr19:36704600-36707600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:36704600-36707800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:36704600-36708000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:36704800-36707400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:36704800-36707600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr19:36704800-36707600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:36704800-36707600	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:36704800-36707600	Active TSS	Psoas Muscle	Psoas
14	chr19:36704800-36707800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:36704800-36707800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:36704800-36708400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:36705000-36707400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:36705000-36707600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:36705000-36707800	Active TSS	HSMMtube	muscle
20	chr19:36705200-36707200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:36705200-36707200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:36705200-36707200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:36705200-36707200	Active TSS	Fetal Muscle Leg	muscle
24	chr19:36705200-36707200	Active TSS	Fetal Stomach	stomach
25	chr19:36705200-36707200	Active TSS	NHEK	skin
26	chr19:36705200-36707400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:36705200-36707400	Active TSS	Fetal Brain Female	brain
28	chr19:36705200-36707400	Active TSS	HSMM	muscle
29	chr19:36705200-36707600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:36705200-36707600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr19:36705200-36707600	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr19:36705200-36707600	Active TSS	Right Ventricle	heart
33	chr19:36705200-36707600	Active TSS	Hela-S3	cervix
34	chr19:36705200-36707600	Active TSS	HMEC	breast
35	chr19:36705200-36707600	Active TSS	NHLF	lung
36	chr19:36705200-36708000	Active TSS	H9 Cell Line	embryonic stem cell
37	chr19:36705200-36708200	Active TSS	K562	blood
38	chr19:36705400-36707200	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr19:36705400-36707400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:36705400-36707400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:36705400-36707400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:36705400-36707400	Active TSS	GM12878-XiMat	blood
43	chr19:36705400-36707600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr19:36705400-36707800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:36706400-36707200	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr19:36706400-36707200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr19:36706600-36707200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:36706600-36707200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr19:36706600-36707200	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr19:36706600-36707200	Active TSS	Fetal Heart	heart

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