Variant report

Variant	rs2490740
Chromosome Location	chr10:94596356-94596357
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:94595494..94597932-chr10:94606791..94609350,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138190	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1033976	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466167	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736071	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736072	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10748586	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786057	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187183	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1326329	1.00[AFR][1000 genomes]
rs1326331	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326332	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409387	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536329	1.00[AFR][1000 genomes]
rs2025730	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094232	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148361	1.00[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182451	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246370	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246382	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246701	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250393	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]
rs2422070	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422072	0.88[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488062	1.00[ASN][1000 genomes]
rs2490732	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490744	1.00[ASN][1000 genomes]
rs2497322	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497324	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497326	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497327	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497331	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497339	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497348	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497350	1.00[ASN][1000 genomes]
rs4517429	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933241	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933242	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933749	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933752	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583846	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7069070	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7070025	0.88[CEU][hapmap];0.93[GIH][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078376	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082382	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089179	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477130	1.00[AFR][1000 genomes]
rs7893270	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894145	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897839	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7909191	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909581	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913340	0.84[CEU][hapmap];0.93[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs7914859	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835250	1.00[AFR][1000 genomes]
rs860668	1.00[AFR][1000 genomes]
rs9419746	1.00[ASN][1000 genomes]
rs9633695	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973733	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980204	1.00[AFR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2490740	NOC3L	cis	parietal	SCAN
rs2490740	CEP55	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94589000-94598000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:94589400-94599200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr10:94591000-94598800	Weak transcription	Right Atrium	heart
4	chr10:94591600-94597000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:94591600-94602800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:94591600-94602800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:94592200-94605600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr10:94593000-94597200	Weak transcription	Primary T cells from cord blood	blood
9	chr10:94593000-94597200	Weak transcription	Placenta	Placenta
10	chr10:94593200-94597000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:94593400-94598600	Weak transcription	Lung	lung
12	chr10:94593800-94596400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
13	chr10:94594000-94597800	Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr10:94594000-94598000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr10:94594200-94596400	Active TSS	Fetal Muscle Trunk	muscle
16	chr10:94594200-94596600	Active TSS	Fetal Muscle Leg	muscle
17	chr10:94594200-94596600	Active TSS	HSMMtube	muscle
18	chr10:94594400-94598600	Weak transcription	Adipose Nuclei	Adipose
19	chr10:94594600-94596600	Weak transcription	K562	blood
20	chr10:94594600-94599000	Weak transcription	Ovary	ovary
21	chr10:94595200-94596800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr10:94595200-94597000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr10:94595400-94598800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:94595400-94599000	Weak transcription	Osteobl	bone
25	chr10:94595400-94599200	Weak transcription	A549	lung
26	chr10:94595600-94599000	Weak transcription	Hela-S3	cervix
27	chr10:94595600-94599000	Weak transcription	NHLF	lung
28	chr10:94596000-94596600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr10:94596000-94597200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:94596000-94597400	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr10:94596000-94598800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr10:94596200-94597200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:94596200-94598000	Weak transcription	Psoas Muscle	Psoas

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