Variant report

Variant	rs9535407
Chromosome Location	chr13:50512292-50512293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr13:50512285-50513016	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50510078..50512694-chr13:50569483..50571768,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM13-7	chr13:50510782-50513292	NONHSAT033768
2	lnc-TRIM13-7	chr13:50511944-50513226	NONHSAT033769

Variant related genes	Relation type
SPRYD7	TF binding region
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11839292	0.83[YRI][hapmap]
rs2066549	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2066557	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2066558	0.81[ASN][1000 genomes]
rs2066575	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs2066581	0.82[YRI][hapmap]
rs2066585	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2066591	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2242482	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap]
rs2472599	0.84[ASN][1000 genomes]
rs2475837	0.86[ASN][1000 genomes]
rs2740524	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]
rs2740544	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs2740545	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2760911	0.83[YRI][hapmap]
rs2760914	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2803839	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2997624	0.82[ASN][1000 genomes]
rs4548769	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs4942899	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4942901	0.91[ASN][1000 genomes]
rs7336058	0.87[ASN][1000 genomes]
rs7338055	0.93[ASN][1000 genomes]
rs73489861	0.88[ASN][1000 genomes]
rs73489862	0.88[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7986337	0.82[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs9535411	0.83[YRI][hapmap]
rs9535414	0.83[YRI][hapmap]
rs9535416	0.83[YRI][hapmap]
rs9568354	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568357	0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs9568363	0.93[ASN][1000 genomes]
rs9568364	0.93[ASN][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs9596215	0.91[ASN][1000 genomes]
rs9596219	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9596220	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.86[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	esv1836423	chr13:50509784-50514706	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1836704	chr13:50509784-50514706	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1838605	chr13:50509784-50514706	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9535407	TRIM13	cis	cerebellum	SCAN
rs9535407	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs9535407	C13orf1	cis	cerebellum	SCAN
rs9535407	KCNRG	cis	cerebellum	SCAN
rs9535407	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs9535407	RB1	cis	cerebellum	SCAN
rs9535407	KDM1B	trans	parietal	SCAN
rs9535407	TMEM43	trans	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50511400-50512400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr13:50511400-50512400	Weak transcription	HSMMtube	muscle
3	chr13:50511400-50512600	Enhancers	Primary B cells from peripheral blood	blood
4	chr13:50511400-50512600	Enhancers	Fetal Thymus	thymus
5	chr13:50511400-50513000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:50511400-50537800	Weak transcription	Left Ventricle	heart
7	chr13:50511600-50512400	Enhancers	Primary B cells from cord blood	blood
8	chr13:50511600-50512400	Weak transcription	Brain Germinal Matrix	brain
9	chr13:50511600-50512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr13:50511600-50512600	Weak transcription	Esophagus	oesophagus
11	chr13:50511600-50512600	Weak transcription	Ovary	ovary
12	chr13:50511600-50512600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr13:50511600-50512600	Enhancers	Stomach Mucosa	stomach
14	chr13:50511600-50512800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr13:50511600-50512800	Weak transcription	NHLF	lung
16	chr13:50511600-50513000	Enhancers	Primary hematopoietic stem cells	blood
17	chr13:50511600-50513000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr13:50511600-50513000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr13:50511600-50513000	Weak transcription	Fetal Kidney	kidney
20	chr13:50511600-50513400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:50511600-50513400	Enhancers	Brain Anterior Caudate	brain
22	chr13:50511600-50513800	Enhancers	HepG2	liver
23	chr13:50511600-50514600	Enhancers	Fetal Intestine Large	intestine
24	chr13:50511600-50517800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr13:50511800-50512400	Enhancers	Liver	Liver
26	chr13:50511800-50512400	Weak transcription	Colonic Mucosa	Colon
27	chr13:50511800-50512400	Enhancers	Duodenum Mucosa	Duodenum
28	chr13:50511800-50512400	Weak transcription	Fetal Muscle Leg	muscle
29	chr13:50511800-50512600	Weak transcription	Fetal Lung	lung
30	chr13:50511800-50512800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr13:50511800-50512800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr13:50511800-50513200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr13:50511800-50513400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr13:50511800-50514200	Enhancers	Fetal Intestine Small	intestine
35	chr13:50512000-50512400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr13:50512000-50512800	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr13:50512200-50512600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr13:50512200-50512600	Active TSS	GM12878-XiMat	blood
39	chr13:50512200-50512800	Enhancers	Pancreas	Pancrea
40	chr13:50512200-50513200	Weak transcription	Fetal Heart	heart
41	chr13:50512200-50514000	Enhancers	Adipose Nuclei	Adipose

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