Variant report

Variant	rs2740524
Chromosome Location	chr13:50593832-50593833
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50588007..50590638-chr13:50592975..50595770,2	MCF-7	breast:
2	chr13:50593013..50597932-chr13:50600321..50603679,5	K562	blood:
3	chr13:50588178..50590212-chr13:50592623..50594133,2	K562	blood:
4	chr13:50570936..50573189-chr13:50591064..50593867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204977	Chromatin interaction
ENSG00000198553	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2066549	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2066557	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066558	0.93[ASN][1000 genomes]
rs2066571	0.81[ASN][1000 genomes]
rs2066572	0.91[ASN][1000 genomes]
rs2066575	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2066585	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2066587	0.83[ASN][1000 genomes]
rs2066591	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2242482	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2687950	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2687951	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2740508	0.85[ASN][1000 genomes]
rs2740544	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2760914	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2803839	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2812222	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2997624	0.85[ASN][1000 genomes]
rs4548769	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4942899	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4942901	0.85[ASN][1000 genomes]
rs7338055	0.81[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7986337	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9535407	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568354	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9568357	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs9568363	0.83[ASN][1000 genomes]
rs9568364	0.83[ASN][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9596215	0.82[ASN][1000 genomes]
rs9596219	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9596220	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2740524	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs2740524	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50573000-50594600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:50574000-50599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:50577600-50594200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:50577600-50594400	Weak transcription	Fetal Brain Male	brain
5	chr13:50578000-50596000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr13:50578600-50604200	Strong transcription	Dnd41	blood
7	chr13:50578600-50629800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:50578800-50654400	Weak transcription	Esophagus	oesophagus
9	chr13:50579000-50597200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:50579000-50598000	Weak transcription	Pancreas	Pancrea
11	chr13:50581800-50602800	Strong transcription	Fetal Thymus	thymus
12	chr13:50582200-50603600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr13:50584400-50599800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr13:50586800-50594600	Weak transcription	Lung	lung
15	chr13:50586800-50595600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:50586800-50601800	Weak transcription	Gastric	stomach
17	chr13:50586800-50654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr13:50587000-50594200	Weak transcription	A549	lung
19	chr13:50587000-50594400	Weak transcription	Fetal Kidney	kidney
20	chr13:50587000-50594600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:50587000-50594600	Weak transcription	Colonic Mucosa	Colon
22	chr13:50587000-50598200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:50587000-50603800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:50587000-50633800	Weak transcription	Hela-S3	cervix
25	chr13:50587000-50645600	Weak transcription	Spleen	Spleen
26	chr13:50587200-50597600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr13:50587200-50617000	Weak transcription	HepG2	liver
28	chr13:50587400-50597400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr13:50587400-50607600	Weak transcription	Psoas Muscle	Psoas
30	chr13:50587600-50594000	Weak transcription	Placenta	Placenta
31	chr13:50587800-50597400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr13:50588000-50645600	Weak transcription	Ovary	ovary
33	chr13:50588400-50594400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr13:50588400-50594400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr13:50589200-50597400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr13:50589400-50594200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr13:50589600-50596200	Weak transcription	NHDF-Ad	bronchial
38	chr13:50589800-50594400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr13:50589800-50645600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr13:50590000-50603000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr13:50590000-50624200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr13:50590200-50594000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:50590200-50594400	Weak transcription	Brain Hippocampus Middle	brain
44	chr13:50590200-50594600	Weak transcription	Left Ventricle	heart
45	chr13:50590200-50596800	Weak transcription	Right Ventricle	heart
46	chr13:50590200-50598600	Weak transcription	Right Atrium	heart
47	chr13:50590200-50653600	Weak transcription	Small Intestine	intestine
48	chr13:50590400-50599000	Weak transcription	Brain Angular Gyrus	brain
49	chr13:50590400-50604400	Weak transcription	NHEK	skin
50	chr13:50590600-50594200	Weak transcription	NH-A	brain

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