Variant report

Variant	rs62110450
Chromosome Location	chr19:52802279-52802280
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	POLR2A	chr19:52802152-52802352	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52799793..52802447-chr19:52803288..52807131,4	MCF-7	breast:
2	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:

Variant related genes	Relation type
ZNF480	TF binding region
ENSG00000269102	TF binding region
ENSG00000167554	Chromatin interaction
ENSG00000198464	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11880020	0.94[ASN][1000 genomes]
rs11880474	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12462567	0.83[AFR][1000 genomes]
rs28845817	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62110448	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110449	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103072	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8103182	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv912299	chr19:52795985-52832830	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52800600-52802600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr19:52801200-52813200	ZNF genes & repeats	A549	lung
3	chr19:52801400-52802400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr19:52801400-52802400	Weak transcription	Ovary	ovary
5	chr19:52801400-52802400	Weak transcription	NHEK	skin
6	chr19:52801400-52803200	Weak transcription	Aorta	Aorta
7	chr19:52801400-52803400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:52801400-52804000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:52801400-52804000	Weak transcription	Hela-S3	cervix
10	chr19:52801600-52802400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:52801600-52802400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:52801600-52802400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:52801600-52802400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:52801600-52802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:52801600-52802400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:52801600-52802400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:52801600-52802400	Active TSS	Primary T cells from cord blood	blood
18	chr19:52801600-52802400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:52801600-52802400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr19:52801600-52802400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:52801600-52802400	Enhancers	Fetal Heart	heart
22	chr19:52801600-52802400	Weak transcription	Fetal Thymus	thymus
23	chr19:52801600-52802400	Weak transcription	Left Ventricle	heart
24	chr19:52801600-52802400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:52801600-52802400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:52801600-52802400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:52801600-52802400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr19:52801600-52802400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr19:52801600-52802600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:52801600-52802600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:52801600-52802600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:52801600-52802600	Weak transcription	Esophagus	oesophagus
33	chr19:52801600-52802800	Weak transcription	Psoas Muscle	Psoas
34	chr19:52801600-52803000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:52801600-52803000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:52801600-52803000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:52801600-52803000	Weak transcription	Placenta	Placenta
38	chr19:52801600-52803200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr19:52801600-52803200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:52801600-52803200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:52801600-52803200	Weak transcription	Brain Anterior Caudate	brain
42	chr19:52801600-52803200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr19:52801600-52803200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr19:52801600-52803200	Weak transcription	Fetal Kidney	kidney
45	chr19:52801600-52803200	Weak transcription	Lung	lung
46	chr19:52801600-52803200	Weak transcription	Pancreas	Pancrea
47	chr19:52801600-52803200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr19:52801600-52803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:52801600-52803400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr19:52801600-52803400	Weak transcription	Adipose Nuclei	Adipose

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