Variant report

Variant	rs12972727
Chromosome Location	chr19:36705054-36705055
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	MAZ	chr19:36704845-36706502	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr19:36704895-36706786	K562	blood:	n/a	n/a
3	REST	chr19:36704763-36707048	H1-neurons	neurons:	n/a	chr19:36705953-36705966 chr19:36705449-36705459 chr19:36705169-36705178
4	POLR2A	chr19:36704892-36707104	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:36704891-36705711	GM12892	blood:	n/a	n/a
6	CHD2	chr19:36704816-36706228	GM12878	blood:	n/a	chr19:36705832-36705842
7	POLR2A	chr19:36704888-36705667	GM12891	blood:	n/a	n/a
8	MXI1	chr19:36704643-36707239	SK-N-SH	brain:	n/a	chr19:36706077-36706086
9	POLR2A	chr19:36705009-36706569	H1-neurons	neurons:	n/a	n/a
10	CREB1	chr19:36704877-36706321	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:36704904-36707081	PFSK-1	brain:	n/a	n/a
12	CREB1	chr19:36704871-36706373	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr19:36704978-36706455	A549	lung:	n/a	n/a
14	POLR2A	chr19:36705014-36706497	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:36705012-36708000	PANC-1	pancreas:	n/a	n/a
16	PAX5	chr19:36704907-36705671	GM12878	blood:	n/a	n/a
17	RELA	chr19:36704865-36706518	GM19099	blood:	n/a	n/a
18	MXI1	chr19:36704688-36707015	IMR90	lung:	n/a	chr19:36706077-36706086
19	MAX	chr19:36704752-36706489	ECC-1	luminal epithelium:	n/a	n/a
20	KAP1	chr19:36704865-36706406	HEK293	kidney:	n/a	n/a
21	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
22	MAFK	chr19:36705022-36706459	K562	blood:	n/a	n/a
23	POLR2A	chr19:36704947-36707096	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIX5	chr19:36704674-36706934	A549	lung:	n/a	chr19:36706350-36706359 chr19:36705618-36705627 chr19:36705620-36705629 chr19:36705875-36705884 chr19:36705877-36705886
25	CHD1	chr19:36704898-36706923	GM12878	blood:	n/a	chr19:36705832-36705842
26	SP1	chr19:36704900-36706299	GM12878	blood:	n/a	chr19:36705832-36705844 chr19:36705496-36705509 chr19:36705494-36705506 chr19:36705496-36705505 chr19:36705495-36705504 chr19:36705829-36705843 chr19:36705833-36705842 chr19:36705494-36705506
27	MAX	chr19:36704995-36706468	H1-hESC	embryonic stem cell:	n/a	n/a
28	GABPA	chr19:36704740-36706505	A549	lung:	n/a	chr19:36706011-36706022 chr19:36706011-36706025 chr19:36706008-36706022 chr19:36705456-36705465 chr19:36706011-36706020 chr19:36705435-36705449
29	POLR2A	chr19:36704754-36707001	HepG2	liver:	n/a	n/a
30	ZNF384	chr19:36704784-36705060	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:36704968-36706366	MCF-7	breast:	n/a	n/a
32	POLR2A	chr19:36704857-36706877	GM12891	blood:	n/a	n/a
33	BHLHE40	chr19:36704903-36706352	K562	blood:	n/a	chr19:36705449-36705465
34	MAX	chr19:36704875-36706430	GM12878	blood:	n/a	n/a
35	CEBPB	chr19:36705016-36705877	GM12878	blood:	n/a	n/a
36	SIN3AK20	chr19:36704978-36706563	MCF-7	breast:	n/a	n/a
37	KAP1	chr19:36704911-36707082	U2OS	brain:	n/a	n/a
38	MAX	chr19:36705034-36706618	ECC-1	luminal epithelium:	n/a	n/a
39	NFATC1	chr19:36704756-36705372	GM12878	blood:	n/a	n/a
40	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
41	STAT5A	chr19:36704464-36706668	GM12878	blood:	n/a	chr19:36705835-36705847 chr19:36705834-36705846
42	PBX3	chr19:36704955-36705285	GM12878	blood:	n/a	n/a
43	USF1	chr19:36704902-36705505	A549	lung:	n/a	chr19:36705449-36705465
44	MAX	chr19:36704829-36706538	HepG2	liver:	n/a	n/a
45	TBL1XR1	chr19:36705046-36706221	K562	blood:	n/a	n/a
46	REST	chr19:36704653-36707128	A549	lung:	n/a	chr19:36705953-36705966 chr19:36705449-36705459 chr19:36705169-36705178
47	POLR2A	chr19:36704844-36706429	Raji	blood:	n/a	n/a
48	POLR2A	chr19:36704850-36706424	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:36704949-36707020	GM12878	blood:	n/a	n/a
50	MYC	chr19:36705027-36706558	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36679317..36682281-chr19:36704526..36707611,3	MCF-7	breast:
2	chr19:36630278..36632151-chr19:36704046..36706551,3	MCF-7	breast:
3	chr19:36704317..36708058-chr19:36719298..36721271,3	MCF-7	breast:
4	chr19:36630466..36632159-chr19:36704253..36707369,3	K562	blood:
5	chr19:36704032..36706423-chr19:36978429..36980490,2	MCF-7	breast:
6	chr19:36704170..36706461-chr19:36978975..36980989,3	K562	blood:
7	chr19:36704361..36705921-chr19:37063810..37066277,2	K562	blood:
8	chr19:36629887..36633258-chr19:36704150..36708473,10	K562	blood:
9	chr19:36705027..36707515-chr19:37176765..37178367,2	MCF-7	breast:

Variant related genes	Relation type
ZNF146	TF binding region
ZNF565	TF binding region
ENSG00000167635	Chromatin interaction
ENSG00000267309	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000225975	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000264276	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12971293	0.82[EUR][1000 genomes]
rs12979040	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12979571	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12979812	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12981691	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12982577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12985315	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12985455	0.82[EUR][1000 genomes]
rs16960884	0.93[EUR][1000 genomes]
rs16970932	0.93[EUR][1000 genomes]
rs34072267	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34242075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34409006	0.84[EUR][1000 genomes]
rs34423559	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34521310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34527953	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34579456	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35342321	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35394138	0.82[EUR][1000 genomes]
rs35747960	0.88[EUR][1000 genomes]
rs35813323	0.93[EUR][1000 genomes]
rs35927732	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35989746	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71354126	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71354130	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7258851	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8104927	0.84[EUR][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

No data

Chromatin state (count:127 , 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	chr19:36704600-36705200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr19:36704600-36705200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:36704600-36705200	Flanking Active TSS	Brain Angular Gyrus	brain
5	chr19:36704600-36705200	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr19:36704600-36705200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
7	chr19:36704600-36705200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:36704600-36705200	Flanking Active TSS	Brain Substantia Nigra	brain
9	chr19:36704600-36705200	Flanking Active TSS	Pancreas	Pancrea
10	chr19:36704600-36705200	Flanking Active TSS	Hela-S3	cervix
11	chr19:36704600-36705200	Flanking Active TSS	K562	blood
12	chr19:36704600-36705200	Flanking Active TSS	NHEK	skin
13	chr19:36704600-36705200	Flanking Active TSS	NHLF	lung
14	chr19:36704600-36705400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr19:36704600-36705400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:36704600-36705400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:36704600-36705400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:36704600-36705400	Flanking Active TSS	Dnd41	blood
19	chr19:36704600-36705400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr19:36704600-36707200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:36704600-36707200	Active TSS	NH-A	brain
22	chr19:36704600-36707400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:36704600-36707400	Active TSS	A549	lung
24	chr19:36704600-36707600	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr19:36704600-36707800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr19:36704600-36708000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:36704800-36705200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:36704800-36705200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:36704800-36705200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:36704800-36705200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr19:36704800-36705200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:36704800-36705200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr19:36704800-36705200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:36704800-36705200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:36704800-36705200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr19:36704800-36705200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:36704800-36705200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:36704800-36705200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:36704800-36705200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr19:36704800-36705200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:36704800-36705200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:36704800-36705200	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr19:36704800-36705200	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr19:36704800-36705200	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr19:36704800-36705200	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr19:36704800-36705200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr19:36704800-36705200	Flanking Active TSS	Esophagus	oesophagus
48	chr19:36704800-36705200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr19:36704800-36705200	Flanking Active TSS	Fetal Brain Female	brain
50	chr19:36704800-36705200	Flanking Active TSS	Fetal Heart	heart

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