Variant report

Variant	rs2803839
Chromosome Location	chr13:50573919-50573920
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:50573061-50574122	MCF-7	breast:	n/a	n/a
2	POLR2A	chr13:50573382-50575037	K562	blood:	n/a	n/a
3	POLR2A	chr13:50573358-50574036	GM12878	blood:	n/a	n/a
4	IRF1	chr13:50573881-50573926	K562	blood:	n/a	n/a
5	POLR2A	chr13:50573009-50573991	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr13:50573653-50574202	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr13:50573660-50573972	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr13:50572923-50573983	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr13:50569571-50574166	GM12891	blood:	n/a	n/a
10	POLR2A	chr13:50573278-50574094	U87	brain:	n/a	n/a
11	POLR2A	chr13:50573202-50575173	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50572788..50574418-chr13:50579406..50581918,2	MCF-7	breast:
2	chr13:50572525..50574239-chr13:50585255..50587483,2	MCF-7	breast:
3	chr13:50573435..50577659-chr13:50588314..50591580,3	K562	blood:
4	chr13:50572352..50574935-chr13:50588640..50591580,2	K562	blood:
5	chr13:50569462..50575212-chr13:50651363..50657415,15	K562	blood:

No data

Variant related genes	Relation type
TRIM13	TF binding region
MIR3613	TF binding region
ENSG00000176124	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000198553	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1326120	0.91[AMR][1000 genomes]
rs2066549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066557	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2066558	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066572	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066587	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066591	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2066594	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2242482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2687950	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2687951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2740508	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2740524	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2740544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812204	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2812216	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2812217	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2812222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2997624	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4548769	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4942899	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336058	0.85[ASN][1000 genomes]
rs7338055	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap]
rs7986337	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs9535407	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9568354	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9568357	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs9568363	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568364	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs9596215	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9596219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596220	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2803839	PHF11	cis	cerebellum	SCAN
rs2803839	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs2803839	KCNRG	cis	cerebellum	SCAN
rs2803839	DLEU2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50570000-50574000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr13:50571800-50585200	Weak transcription	Gastric	stomach
3	chr13:50572000-50574600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:50572000-50574600	Enhancers	Stomach Mucosa	stomach
5	chr13:50572000-50574800	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr13:50572000-50578400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:50572000-50578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:50572000-50585800	Weak transcription	Ovary	ovary
9	chr13:50572200-50574200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
10	chr13:50572200-50574400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:50572200-50574400	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr13:50572200-50574600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
13	chr13:50572200-50574600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:50572400-50574000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:50572400-50574200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
16	chr13:50572400-50574200	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr13:50572400-50574800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr13:50572400-50574800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr13:50572400-50574800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:50572400-50574800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
21	chr13:50572600-50574000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:50572600-50574200	Enhancers	Primary hematopoietic stem cells	blood
23	chr13:50572600-50574200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:50572600-50574200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr13:50572600-50574200	Genic enhancers	Fetal Muscle Leg	muscle
26	chr13:50572600-50574200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
27	chr13:50572600-50574400	Enhancers	Brain Angular Gyrus	brain
28	chr13:50572600-50574600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr13:50572600-50574600	Genic enhancers	Fetal Lung	lung
30	chr13:50572600-50574800	Genic enhancers	Adipose Nuclei	Adipose
31	chr13:50572600-50574800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr13:50572600-50574800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr13:50572600-50575600	Genic enhancers	Fetal Intestine Small	intestine
34	chr13:50572600-50577600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr13:50572600-50578400	Weak transcription	Esophagus	oesophagus
36	chr13:50572600-50579200	Weak transcription	HSMMtube	muscle
37	chr13:50572600-50589600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:50572800-50574000	Genic enhancers	Placenta Amnion	Placenta Amnion
39	chr13:50572800-50574000	Genic enhancers	NHDF-Ad	bronchial
40	chr13:50572800-50574200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
41	chr13:50572800-50574200	Enhancers	Brain Cingulate Gyrus	brain
42	chr13:50572800-50574200	Enhancers	Right Atrium	heart
43	chr13:50572800-50574200	Genic enhancers	HepG2	liver
44	chr13:50572800-50574200	Enhancers	HMEC	breast
45	chr13:50572800-50574400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:50572800-50574400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
47	chr13:50572800-50574800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr13:50572800-50574800	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr13:50572800-50574800	Genic enhancers	NHEK	skin
50	chr13:50572800-50575000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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