Variant report

Variant	rs73934407
Chromosome Location	chr19:52803224-52803225
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	POLR2A	chr19:52803117-52803555	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52799531..52802059-chr19:52803187..52805101,2	K562	blood:
2	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:

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

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10409071	1.00[ASN][1000 genomes]
rs10416397	1.00[ASN][1000 genomes]
rs11537695	1.00[ASN][1000 genomes]
rs13382052	1.00[ASN][1000 genomes]
rs2061355	1.00[ASN][1000 genomes]
rs41275796	1.00[ASN][1000 genomes]
rs41275802	1.00[ASN][1000 genomes]
rs56071533	1.00[ASN][1000 genomes]
rs58576324	1.00[ASN][1000 genomes]
rs61285115	1.00[ASN][1000 genomes]
rs717322	1.00[ASN][1000 genomes]
rs73934406	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73935029	1.00[ASN][1000 genomes]
rs73935031	1.00[ASN][1000 genomes]
rs73935032	1.00[ASN][1000 genomes]
rs73935039	1.00[ASN][1000 genomes]
rs73935040	1.00[ASN][1000 genomes]
rs73935041	1.00[ASN][1000 genomes]
rs73935044	1.00[ASN][1000 genomes]
rs73935048	1.00[ASN][1000 genomes]
rs73935050	1.00[ASN][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	chr19:52801200-52813200	ZNF genes & repeats	A549	lung
2	chr19:52801400-52803400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:52801400-52804000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:52801400-52804000	Weak transcription	Hela-S3	cervix
5	chr19:52801600-52803400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:52801600-52803400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:52801600-52803400	Weak transcription	Adipose Nuclei	Adipose
8	chr19:52801600-52803400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:52801600-52803400	Weak transcription	Gastric	stomach
10	chr19:52801600-52803400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:52801600-52803400	Weak transcription	HMEC	breast
12	chr19:52801600-52803600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:52801600-52803600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr19:52801600-52803600	Weak transcription	Brain Hippocampus Middle	brain
15	chr19:52801600-52803600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr19:52801600-52803600	Weak transcription	Right Ventricle	heart
17	chr19:52801600-52803600	Weak transcription	HSMMtube	muscle
18	chr19:52801600-52803600	Weak transcription	HUVEC	blood vessel
19	chr19:52801600-52803600	Weak transcription	NHLF	lung
20	chr19:52801600-52803800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:52801600-52803800	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:52801600-52803800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:52801600-52803800	Weak transcription	Osteobl	bone
24	chr19:52801600-52804000	Weak transcription	HSMM	muscle
25	chr19:52801600-52804000	Weak transcription	NHDF-Ad	bronchial
26	chr19:52801600-52804200	Weak transcription	Brain Angular Gyrus	brain
27	chr19:52801600-52806000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
28	chr19:52801600-52808800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:52801800-52803800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr19:52801800-52804800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr19:52801800-52805600	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr19:52801800-52827200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:52801800-52829200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:52802000-52804000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:52802000-52804200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:52802000-52804400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:52802000-52804600	ZNF genes & repeats	K562	blood
38	chr19:52802000-52806400	ZNF genes & repeats	Thymus	Thymus
39	chr19:52802000-52806800	ZNF genes & repeats	GM12878-XiMat	blood
40	chr19:52802000-52808800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:52802000-52813200	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr19:52802000-52826400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:52802000-52830000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:52802200-52803400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:52802200-52803400	Weak transcription	Fetal Brain Male	brain
46	chr19:52802200-52803600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:52802200-52803600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:52802200-52803600	Weak transcription	HepG2	liver
49	chr19:52802200-52804200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:52802200-52804600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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