Variant report

Variant	rs9285179
Chromosome Location	chr13:52168793-52168794
allele	G/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	GATA1	chr13:52168552-52169066	PBDE	blood:	n/a	chr13:52168778-52168791
2	CEBPD	chr13:52168553-52168917	K562	blood:	n/a	n/a
3	RCOR1	chr13:52168698-52168978	K562	blood:	n/a	n/a
4	TAL1	chr13:52168596-52168976	K562	blood:	n/a	n/a
5	TEAD4	chr13:52168601-52168870	K562	blood:	n/a	n/a
6	TEAD4	chr13:52168561-52169012	K562	blood:	n/a	n/a
7	EP300	chr13:52168726-52168886	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52161931..52163460-chr13:52168528..52170984,2	K562	blood:
2	chr13:52167123..52169021-chr13:52171538..52173989,2	MCF-7	breast:

Variant related genes	Relation type
ATP5F1P1	TF binding region
RN7SL413P	TF binding region
ENSG00000224451	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

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];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4456399	0.81[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.83[ASN][1000 genomes]
rs4533167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943008	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]
rs4943014	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6561644	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7320201	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7327107	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7984225	0.82[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[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];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9526792	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9535716	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535720	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.82[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];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9285179	TRIM13	cis	cerebellum	SCAN
rs9285179	WDFY2	cis	multi-tissue	Pritchard
rs9285179	WDFY2	cis	parietal	SCAN
rs9285179	THSD1P1	cis	cerebellum	SCAN
rs9285179	FLJ13639	cis	multi-tissue	Pritchard

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52159600-52170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:52159600-52174600	Weak transcription	Spleen	Spleen
3	chr13:52160200-52170800	Weak transcription	Fetal Intestine Small	intestine
4	chr13:52160200-52181400	Weak transcription	Thymus	Thymus
5	chr13:52160400-52173400	Weak transcription	Right Atrium	heart
6	chr13:52160400-52177000	Weak transcription	Right Ventricle	heart
7	chr13:52160600-52169400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr13:52160600-52172200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr13:52161400-52168800	Weak transcription	Fetal Brain Female	brain
10	chr13:52162800-52180200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:52163000-52170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr13:52163200-52182600	Weak transcription	Ovary	ovary
13	chr13:52164200-52169200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr13:52165400-52168800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:52165400-52169200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:52165400-52169200	Weak transcription	Esophagus	oesophagus
17	chr13:52165400-52169200	Weak transcription	Gastric	stomach
18	chr13:52165400-52174200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr13:52165600-52169200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:52165600-52170600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:52165600-52170600	Weak transcription	Psoas Muscle	Psoas
22	chr13:52165600-52173400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:52165600-52173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:52165600-52188600	Weak transcription	Fetal Stomach	stomach
25	chr13:52165800-52169200	Weak transcription	Fetal Brain Male	brain
26	chr13:52165800-52169400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr13:52165800-52169400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr13:52165800-52170600	Weak transcription	Fetal Kidney	kidney
29	chr13:52165800-52173200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:52165800-52179000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:52166000-52168800	Weak transcription	Brain Hippocampus Middle	brain
32	chr13:52166000-52168800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr13:52166000-52169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr13:52166000-52170600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:52166000-52170800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:52166000-52172600	Weak transcription	Adipose Nuclei	Adipose
37	chr13:52166000-52172600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr13:52166000-52173600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr13:52166000-52175800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:52166000-52176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr13:52166000-52181200	Weak transcription	NH-A	brain
42	chr13:52166200-52168800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:52166200-52168800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr13:52166200-52168800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr13:52166200-52168800	Weak transcription	Aorta	Aorta
46	chr13:52166200-52169200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr13:52166200-52169200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr13:52166200-52169200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:52166200-52169600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:52166200-52169600	Weak transcription	Brain Anterior Caudate	brain

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