Variant report

Variant	rs3733828
Chromosome Location	chr19:41310609-41310610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41309782-41310885	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:41309410-41311937	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:41308529-41310616	HL-60	blood:	n/a	n/a
4	POLR2A	chr19:41308428-41312038	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:41310121-41310611	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr19:41310580-41310730	HVMF	connective:	n/a	n/a
7	CTCF	chr19:41310540-41310690	A549	lung:	n/a	n/a
8	POLR2A	chr19:41308880-41317807	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:41309752-41318497	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr19:41308407-41313533	K562	blood:	n/a	n/a
11	POLR2A	chr19:41307117-41318353	K562	blood:	n/a	n/a
12	POLR2A	chr19:41307663-41316128	GM12892	blood:	n/a	n/a
13	CTCF	chr19:41310560-41310710	NHEK	skin:	n/a	n/a
14	CTCF	chr19:41310600-41310750	HRE	kidney:	n/a	n/a
15	POLR2A	chr19:41310388-41311012	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:41309282-41311365	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr19:41310587-41311144	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr19:41307671-41311968	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:41307768-41311357	K562	blood:	n/a	n/a
20	POLR2A	chr19:41310202-41310615	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:41309721-41310628	GM12892	blood:	n/a	n/a
22	POLR2A	chr19:41307876-41312060	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:41307781-41314972	GM12891	blood:	n/a	n/a
24	CTCF	chr19:41310560-41310710	HCM	heart:	n/a	n/a
25	POLR2A	chr19:41307556-41311130	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:41310170-41311308	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr19:41309515-41312290	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:41308762-41311163	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr19:41308432-41316432	K562	blood:	n/a	n/a
30	POLR2A	chr19:41307640-41313313	K562	blood:	n/a	n/a
31	POLR2A	chr19:41307839-41311076	GM12878	blood:	n/a	n/a
32	POLR2A	chr19:41308985-41316368	A549	lung:	n/a	n/a
33	CTCF	chr19:41310540-41310690	HVMF	connective:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41282962..41284842-chr19:41308232..41310693,2	MCF-7	breast:
2	chr19:41310513..41314653-chr19:41415794..41419669,4	K562	blood:
3	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:
4	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
5	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
6	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
7	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
8	chr19:41221436..41223725-chr19:41310201..41314445,5	MCF-7	breast:

No data

Variant related genes	Relation type
EGLN2	TF binding region
ENSG00000261857	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000198251	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2644916	0.83[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs4803372	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3733828	CCDC9	cis	cerebellum	SCAN
rs3733828	ZNF235	cis	parietal	SCAN
rs3733828	FLT3LG	cis	cerebellum	SCAN
rs3733828	ADCK4	cis	multi-tissue	Pritchard
rs3733828	NKPD1	cis	cerebellum	SCAN
rs3733828	ZNF780A	cis	lymphoblastoid	seeQTL
rs3733828	LIN7B	cis	parietal	SCAN
rs3733828	KCNN4	cis	cerebellum	SCAN
rs3733828	ADCK4	cis	lymphoblastoid	seeQTL
rs3733828	LYPD5	cis	cerebellum	SCAN
rs3733828	LMTK3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41305800-41316200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41306000-41311800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:41306200-41311200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
4	chr19:41306200-41313200	Enhancers	Fetal Heart	heart
5	chr19:41306400-41311200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
6	chr19:41306400-41313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:41306400-41313800	Genic enhancers	Fetal Thymus	thymus
8	chr19:41306400-41316200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:41306400-41316800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:41306600-41311200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
11	chr19:41306600-41311800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr19:41306600-41312400	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr19:41306600-41314000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:41306600-41314800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:41306800-41311200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:41306800-41312200	Weak transcription	HSMMtube	muscle
17	chr19:41306800-41313400	Genic enhancers	Gastric	stomach
18	chr19:41307000-41312400	Enhancers	Small Intestine	intestine
19	chr19:41307000-41313400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
20	chr19:41307000-41315800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:41307200-41311200	Genic enhancers	Thymus	Thymus
22	chr19:41307200-41312400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
23	chr19:41307400-41311600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:41307800-41311000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr19:41307800-41311800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr19:41307800-41311800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:41308000-41311400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:41308000-41311800	Enhancers	Ovary	ovary
29	chr19:41308000-41313600	Weak transcription	Aorta	Aorta
30	chr19:41308200-41311200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
31	chr19:41308200-41312000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:41308200-41313200	Enhancers	Liver	Liver
33	chr19:41308200-41313400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr19:41308400-41310800	Enhancers	Fetal Lung	lung
35	chr19:41308400-41311200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr19:41308400-41311400	Weak transcription	Fetal Kidney	kidney
37	chr19:41308400-41311400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr19:41308400-41313600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:41308400-41313600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:41308400-41316400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:41308600-41311200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:41308600-41312000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr19:41308600-41313600	Enhancers	Psoas Muscle	Psoas
44	chr19:41308800-41310800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:41308800-41310800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr19:41308800-41312200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr19:41308800-41312200	Genic enhancers	NHEK	skin
48	chr19:41308800-41312400	Enhancers	Brain Substantia Nigra	brain
49	chr19:41308800-41313200	Enhancers	Pancreas	Pancrea
50	chr19:41308800-41313400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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