Variant report

Variant	rs2407804
Chromosome Location	chr13:50362098-50362099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50356308..50362290-chr13:50362376..50368273,10	K562	blood:
2	chr13:50358890..50362545-chr13:50364885..50368463,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10492591	0.84[AMR][1000 genomes]
rs1127021	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1198315	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1198319	0.81[EUR][1000 genomes]
rs1198320	0.81[EUR][1000 genomes]
rs1201716	0.81[EUR][1000 genomes]
rs1407440	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1407441	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1547623	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1581745	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1885724	0.83[AFR][1000 genomes]
rs2025263	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2181185	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2897770	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3851162	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4942863	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7330392	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7983303	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7984061	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9316474	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9526591	0.87[EUR][1000 genomes]
rs9526593	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9535305	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9535307	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9535310	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9535316	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9535330	0.85[AFR][1000 genomes]
rs9535340	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535341	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9562927	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

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	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv900075	chr13:50331992-50376858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2407804	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
3	chr13:50336800-50364600	Weak transcription	NHLF	lung
4	chr13:50349600-50365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:50349600-50365400	Weak transcription	Lung	lung
6	chr13:50351200-50364200	Weak transcription	HSMM	muscle
7	chr13:50351200-50364600	Weak transcription	HSMMtube	muscle
8	chr13:50351400-50362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:50351400-50363000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr13:50351600-50363800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr13:50351800-50363800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:50351800-50364000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:50352000-50365200	Weak transcription	Fetal Thymus	thymus
14	chr13:50352400-50364400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr13:50352600-50363800	Weak transcription	Pancreas	Pancrea
16	chr13:50352600-50363800	Weak transcription	Thymus	Thymus
17	chr13:50352600-50364800	Weak transcription	A549	lung
18	chr13:50353000-50363800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr13:50353000-50363800	Weak transcription	Small Intestine	intestine
20	chr13:50353800-50363800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:50354200-50363800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr13:50354200-50363800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr13:50354200-50364400	Weak transcription	Right Atrium	heart
24	chr13:50354200-50365400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr13:50354400-50362600	Weak transcription	Dnd41	blood
26	chr13:50354400-50363200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr13:50354400-50363600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:50354400-50365400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:50354800-50362400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr13:50356000-50363200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:50356200-50363800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr13:50356200-50364800	Weak transcription	NHEK	skin
33	chr13:50356400-50364000	Weak transcription	Brain Anterior Caudate	brain
34	chr13:50356400-50365200	Weak transcription	Right Ventricle	heart
35	chr13:50356600-50363000	Weak transcription	Brain Hippocampus Middle	brain
36	chr13:50356600-50365000	Weak transcription	Fetal Kidney	kidney
37	chr13:50356800-50363200	Weak transcription	Brain Germinal Matrix	brain
38	chr13:50356800-50364600	Weak transcription	Primary B cells from cord blood	blood
39	chr13:50357000-50363600	Weak transcription	Fetal Brain Female	brain
40	chr13:50357000-50364400	Weak transcription	Ovary	ovary
41	chr13:50357800-50363000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr13:50357800-50363200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:50357800-50364000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr13:50357800-50364200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:50357800-50364600	Weak transcription	Fetal Stomach	stomach
46	chr13:50357800-50365200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:50358000-50362600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:50358400-50363800	Weak transcription	Left Ventricle	heart
49	chr13:50358400-50364400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:50358400-50364600	Weak transcription	Aorta	Aorta

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