Variant report

Variant	rs4943008
Chromosome Location	chr13:52170618-52170619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52165459..52167828-chr13:52169558..52171705,2	K562	blood:
2	chr13:52162017..52163554-chr13:52169450..52171353,2	MCF-7	breast:
3	chr13:52161931..52163460-chr13:52168528..52170984,2	K562	blood:
4	chr13:52163928..52166690-chr13:52169600..52171237,2	MCF-7	breast:
5	chr13:52026784..52028994-chr13:52169787..52172017,2	MCF-7	breast:
6	chr13:52023038..52025684-chr13:52169375..52171570,2	K562	blood:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1885855	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1923874	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4456399	0.81[ASW][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.83[ASN][1000 genomes]
rs4533167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943014	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561644	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7320201	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7327107	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7984225	0.82[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7988297	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7990679	0.88[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9285179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526792	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9535716	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535720	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568642	0.83[MEX][hapmap]
rs992583	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4943008	TRIM13	cis	cerebellum	SCAN
rs4943008	THSD1P1	cis	cerebellum	SCAN
rs4943008	WDFY2	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52159600-52174600	Weak transcription	Spleen	Spleen
2	chr13:52160200-52170800	Weak transcription	Fetal Intestine Small	intestine
3	chr13:52160200-52181400	Weak transcription	Thymus	Thymus
4	chr13:52160400-52173400	Weak transcription	Right Atrium	heart
5	chr13:52160400-52177000	Weak transcription	Right Ventricle	heart
6	chr13:52160600-52172200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr13:52162800-52180200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:52163200-52182600	Weak transcription	Ovary	ovary
9	chr13:52165400-52174200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr13:52165600-52173400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr13:52165600-52173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr13:52165600-52188600	Weak transcription	Fetal Stomach	stomach
13	chr13:52165800-52173200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:52165800-52179000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:52166000-52170800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:52166000-52172600	Weak transcription	Adipose Nuclei	Adipose
17	chr13:52166000-52172600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr13:52166000-52173600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:52166000-52175800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:52166000-52176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr13:52166000-52181200	Weak transcription	NH-A	brain
22	chr13:52166200-52173400	Weak transcription	GM12878-XiMat	blood
23	chr13:52166200-52175600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:52166200-52178800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr13:52166200-52181200	Weak transcription	NHLF	lung
26	chr13:52166400-52170800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:52166400-52176200	Weak transcription	Osteobl	bone
28	chr13:52166400-52181200	Weak transcription	Hela-S3	cervix
29	chr13:52166600-52173400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:52167200-52173400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:52167600-52179800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:52168200-52171400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr13:52168200-52172000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr13:52168400-52177400	Weak transcription	Lung	lung
35	chr13:52168400-52194400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr13:52168600-52170800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr13:52168600-52171200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:52168600-52174400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr13:52168600-52177600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr13:52168800-52171200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr13:52168800-52173600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr13:52169200-52172200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr13:52169200-52172200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr13:52169200-52174000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr13:52169400-52171000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr13:52169400-52173400	Weak transcription	Brain Angular Gyrus	brain
47	chr13:52169400-52174600	Weak transcription	Aorta	Aorta
48	chr13:52169600-52170800	Enhancers	Brain Anterior Caudate	brain
49	chr13:52169600-52171200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:52169600-52174400	Weak transcription	K562	blood

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