Variant report

Variant	rs2432040
Chromosome Location	chr19:36707317-36707318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36705012-36708000	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:36707147-36707374	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr19:36704580-36707460	IMR90	lung:	n/a	chr19:36706939-36706949 chr19:36705832-36705842
4	POLR2A	chr19:36707206-36708042	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:36707111-36708050	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:36707236-36707553	K562	blood:	n/a	n/a
7	POLR2A	chr19:36704767-36707348	IMR90	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10416729	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11673662	0.92[ASN][1000 genomes]
rs12460237	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12608941	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1898675	0.83[ASN][1000 genomes]
rs2432044	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2432046	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2432048	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2432050	0.89[ASN][1000 genomes]
rs2432053	0.94[ASN][1000 genomes]
rs2438515	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2438516	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2910681	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918322	0.87[ASN][1000 genomes]
rs2918323	0.81[ASN][1000 genomes]
rs2918324	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918325	0.81[ASN][1000 genomes]
rs2918376	0.94[ASN][1000 genomes]
rs2918377	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918381	0.92[ASN][1000 genomes]
rs2918383	0.85[ASN][1000 genomes]
rs2918384	0.87[ASN][1000 genomes]
rs2972320	0.87[ASN][1000 genomes]
rs2972528	0.88[EUR][1000 genomes]
rs2972532	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2972533	0.87[ASN][1000 genomes]
rs2972534	0.86[ASN][1000 genomes]
rs2972535	0.92[ASN][1000 genomes]
rs2972536	0.86[ASN][1000 genomes]
rs2972540	0.94[ASN][1000 genomes]
rs2972543	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34912665	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4293497	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4315447	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57614488	0.84[EUR][1000 genomes]
rs60277419	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6510528	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8107260	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8107616	0.82[AMR][1000 genomes];0.89[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2432040	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

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	chr19:36704600-36707400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:36704600-36707400	Active TSS	A549	lung
4	chr19:36704600-36707600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:36704600-36707800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:36704600-36708000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:36704800-36707400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:36704800-36707600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr19:36704800-36707600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:36704800-36707600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:36704800-36707600	Active TSS	Psoas Muscle	Psoas
12	chr19:36704800-36707800	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:36704800-36707800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:36704800-36708400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:36705000-36707400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:36705000-36707600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:36705000-36707800	Active TSS	HSMMtube	muscle
18	chr19:36705200-36707400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:36705200-36707400	Active TSS	Fetal Brain Female	brain
20	chr19:36705200-36707400	Active TSS	HSMM	muscle
21	chr19:36705200-36707600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:36705200-36707600	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr19:36705200-36707600	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr19:36705200-36707600	Active TSS	Right Ventricle	heart
25	chr19:36705200-36707600	Active TSS	Hela-S3	cervix
26	chr19:36705200-36707600	Active TSS	HMEC	breast
27	chr19:36705200-36707600	Active TSS	NHLF	lung
28	chr19:36705200-36708000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr19:36705200-36708200	Active TSS	K562	blood
30	chr19:36705400-36707400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36705400-36707400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:36705400-36707400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:36705400-36707400	Active TSS	GM12878-XiMat	blood
34	chr19:36705400-36707600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:36705400-36707800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:36706600-36707400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:36706600-36707800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr19:36706800-36707400	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr19:36706800-36707400	Weak transcription	Gastric	stomach
40	chr19:36706800-36707400	Weak transcription	Pancreas	Pancrea
41	chr19:36706800-36707400	Weak transcription	Spleen	Spleen
42	chr19:36706800-36707600	Flanking Active TSS	Dnd41	blood
43	chr19:36706800-36707800	Enhancers	Small Intestine	intestine
44	chr19:36706800-36708400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:36706800-36708400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:36706800-36708600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:36706800-36709800	Weak transcription	Lung	lung
48	chr19:36706800-36710800	Weak transcription	Esophagus	oesophagus
49	chr19:36706800-36716400	Weak transcription	Aorta	Aorta
50	chr19:36707000-36707400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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