Variant report

Variant	rs72483956
Chromosome Location	chr19:52801468-52801469
allele	C/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	chr19:52800329-52801682	GM12878	blood:	n/a	n/a
2	MAZ	chr19:52799619-52801613	IMR90	lung:	n/a	n/a
3	MAX	chr19:52800363-52801565	K562	blood:	n/a	n/a
4	POLR2A	chr19:52799967-52801511	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:52800362-52801595	GM12878	blood:	n/a	n/a
6	REST	chr19:52799805-52801604	H1-neurons	neurons:	n/a	chr19:52800663-52800676 chr19:52800568-52800581 chr19:52800838-52800845 chr19:52801431-52801444 chr19:52800751-52800764 chr19:52801427-52801437
7	MXI1	chr19:52799569-52801627	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr19:52801207-52801635	K562	blood:	n/a	n/a
9	POLR2A	chr19:52800309-52801570	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr19:52800028-52801511	IMR90	lung:	n/a	n/a
11	MXI1	chr19:52799779-52801694	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52776723..52778376-chr19:52800239..52801922,2	K562	blood:
2	chr19:52799793..52802447-chr19:52803288..52807131,4	MCF-7	breast:
3	chr19:52772363..52775107-chr19:52799601..52802037,4	MCF-7	breast:
4	chr19:52799531..52802059-chr19:52803187..52805101,2	K562	blood:
5	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269102	TF binding region
ZNF480	TF binding region
ENSG00000196214	Chromatin interaction
ENSG00000167554	Chromatin interaction
ENSG00000198464	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs321910	0.82[ASN][1000 genomes]
rs321911	0.82[ASN][1000 genomes]
rs3810121	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810123	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72483954	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72483955	0.83[AMR][1000 genomes];0.89[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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52799600-52801600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:52799600-52801600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:52799600-52801600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:52799600-52801600	Active TSS	Fetal Kidney	kidney
5	chr19:52799600-52801800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:52799600-52801800	Active TSS	Colonic Mucosa	Colon
7	chr19:52799800-52801600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:52799800-52801600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr19:52799800-52801600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr19:52799800-52801600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:52799800-52801600	Active TSS	Fetal Intestine Large	intestine
12	chr19:52799800-52801600	Active TSS	HSMM	muscle
13	chr19:52799800-52801600	Active TSS	NHDF-Ad	bronchial
14	chr19:52799800-52801800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:52800000-52801600	Active TSS	Fetal Brain Female	brain
16	chr19:52800000-52802000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:52800200-52801600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:52800600-52801600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr19:52800600-52801600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:52800600-52801600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr19:52800600-52802600	Transcr. at gene 5' and 3'	Dnd41	blood
22	chr19:52800800-52801600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr19:52800800-52801600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr19:52800800-52801600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr19:52800800-52801600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:52800800-52801600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:52800800-52801600	Flanking Active TSS	Liver	Liver
28	chr19:52800800-52801600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr19:52800800-52801600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr19:52801000-52801600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:52801000-52801600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr19:52801000-52801600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:52801000-52801600	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr19:52801000-52801600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr19:52801000-52801600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr19:52801000-52801600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr19:52801000-52801600	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr19:52801000-52801600	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr19:52801000-52801600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr19:52801000-52801600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr19:52801000-52801600	Flanking Active TSS	Fetal Heart	heart
42	chr19:52801000-52801600	Flanking Active TSS	Fetal Stomach	stomach
43	chr19:52801000-52801600	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr19:52801000-52801600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr19:52801000-52801600	Flanking Active TSS	NH-A	brain
46	chr19:52801000-52801600	Flanking Active TSS	Osteobl	bone
47	chr19:52801000-52801800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr19:52801000-52801800	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr19:52801000-52801800	Enhancers	Spleen	Spleen
50	chr19:52801000-52802000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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