Variant report

Variant	rs4802906
Chromosome Location	chr19:52735298-52735299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52733968-52735570	U87	brain:	n/a	n/a
2	POLR2A	chr19:52735257-52735426	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:52734690-52735316	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:52733732-52735532	K562	blood:	n/a	n/a
5	POLR2A	chr19:52734774-52735653	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:52733737-52735599	U87	brain:	n/a	n/a
7	POLR2A	chr19:52733795-52735686	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:52733730-52735455	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr19:52733751-52735440	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr19:52733791-52735334	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52692325..52695090-chr19:52733176..52735417,3	MCF-7	breast:
2	chr19:52714640..52717140-chr19:52734016..52736347,2	K562	blood:
3	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268015	TF binding region
ENSG00000105568	Chromatin interaction
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17835915	0.94[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs1864007	1.00[YRI][hapmap]
rs2059810	0.86[ASW][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs4802905	0.88[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4802907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802908	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107718	0.90[JPT][hapmap]
rs8107878	1.00[YRI][hapmap]
rs997703	0.94[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4802906	ZNF446	cis	parietal	SCAN
rs4802906	ZNF497	cis	parietal	SCAN
rs4802906	LENG9	cis	cerebellum	SCAN
rs4802906	ZSCAN18	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52719000-52735400	ZNF genes & repeats	A549	lung
2	chr19:52727600-52737800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:52730200-52737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:52730800-52741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:52731000-52736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:52731000-52736800	Weak transcription	Stomach Mucosa	stomach
7	chr19:52731600-52736400	Weak transcription	Fetal Heart	heart
8	chr19:52731600-52738000	Weak transcription	Fetal Brain Male	brain
9	chr19:52731600-52741000	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:52731800-52735400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr19:52731800-52736600	Weak transcription	HUVEC	blood vessel
12	chr19:52732000-52736000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr19:52732000-52736000	Weak transcription	Psoas Muscle	Psoas
14	chr19:52732000-52736600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:52732000-52740600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:52732000-52740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:52732200-52735600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:52732200-52736000	Weak transcription	Ovary	ovary
19	chr19:52732200-52736000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr19:52732200-52736200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:52732200-52736400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:52732200-52741000	Weak transcription	Dnd41	blood
23	chr19:52732200-52741200	Weak transcription	Fetal Lung	lung
24	chr19:52732400-52735400	Weak transcription	Liver	Liver
25	chr19:52732400-52735400	Weak transcription	HSMMtube	muscle
26	chr19:52732400-52735400	Weak transcription	NHLF	lung
27	chr19:52732400-52735800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:52732400-52735800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:52732400-52735800	Weak transcription	Left Ventricle	heart
30	chr19:52732400-52736000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:52732400-52736000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:52732400-52736400	Weak transcription	Adipose Nuclei	Adipose
33	chr19:52732400-52737800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:52732400-52737800	Weak transcription	HepG2	liver
35	chr19:52732400-52740200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:52732400-52740600	Weak transcription	Brain Angular Gyrus	brain
37	chr19:52732400-52741000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr19:52732400-52741200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:52732600-52736000	Weak transcription	Spleen	Spleen
40	chr19:52732600-52736400	Weak transcription	Fetal Brain Female	brain
41	chr19:52732600-52736800	Weak transcription	Primary T cells from cord blood	blood
42	chr19:52733000-52735600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:52733000-52736000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:52733000-52736200	Weak transcription	Thymus	Thymus
45	chr19:52733000-52736600	Weak transcription	Fetal Intestine Large	intestine
46	chr19:52733000-52736600	Weak transcription	HSMM	muscle
47	chr19:52733000-52736800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:52733000-52737000	Weak transcription	Placenta	Placenta
49	chr19:52733000-52737400	Weak transcription	Colonic Mucosa	Colon
50	chr19:52733200-52735600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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