Variant report

Variant	rs2250393
Chromosome Location	chr10:94610368-94610369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:94607070..94611530-chr10:94637347..94641279,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225118	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1033976	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466167	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736071	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736072	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10748586	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786057	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187183	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1326329	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1326331	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326332	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409387	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536329	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1960367	0.81[AMR][1000 genomes]
rs2025730	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094232	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148361	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182451	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246382	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246701	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422070	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422072	0.88[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488062	1.00[ASN][1000 genomes]
rs2490732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490733	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490740	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490742	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490744	1.00[ASN][1000 genomes]
rs2497322	1.00[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497323	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497324	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497326	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497327	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497331	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497339	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497348	1.00[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497350	1.00[ASN][1000 genomes]
rs4517429	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933241	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933242	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933749	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933752	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583846	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583848	0.82[EUR][1000 genomes]
rs7069070	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7070025	0.88[CEU][hapmap];0.96[GIH][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078376	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082382	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089179	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477130	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7893270	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894145	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897839	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7909191	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909581	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913340	0.84[CEU][hapmap];0.96[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs7914859	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835250	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs860668	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9419746	1.00[ASN][1000 genomes]
rs9633695	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973733	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980204	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2250393	CEP55	cis	cerebellum	SCAN
rs2250393	NOC3L	cis	parietal	SCAN
rs2250393	EXOC6	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94609200-94610400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr10:94609200-94612600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr10:94609200-94614800	Weak transcription	Lung	lung
4	chr10:94609200-94621000	Weak transcription	Pancreas	Pancrea
5	chr10:94609600-94610400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr10:94609600-94610400	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr10:94609600-94610600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:94609600-94611600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr10:94609600-94612000	Weak transcription	Fetal Stomach	stomach
10	chr10:94609600-94622400	Weak transcription	Thymus	Thymus
11	chr10:94609800-94610400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:94609800-94611000	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr10:94609800-94619000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr10:94610000-94610600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:94610000-94610800	Weak transcription	Fetal Brain Female	brain
16	chr10:94610000-94613000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:94610200-94610400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:94610200-94610600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:94610200-94611000	Enhancers	HUVEC	blood vessel
20	chr10:94610200-94613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:94610200-94614400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr10:94610200-94614600	Weak transcription	Primary hematopoietic stem cells	blood

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