Variant report

Variant	rs1409387
Chromosome Location	chr10:94636367-94636368
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	chr10:94634802..94636434-chr10:94636550..94638856,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225118	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1033976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466167	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736071	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736072	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10748586	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786057	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187183	0.86[EUR][1000 genomes]
rs1326329	0.82[EUR][1000 genomes]
rs1326331	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326332	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536329	0.81[EUR][1000 genomes]
rs1960367	0.88[AMR][1000 genomes]
rs2025730	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094232	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148361	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182451	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246370	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246382	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246701	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250393	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]
rs2422070	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422072	0.88[CEU][hapmap];0.96[GIH][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488062	1.00[ASN][1000 genomes]
rs2490732	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490733	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490740	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]
rs2490742	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490744	1.00[ASN][1000 genomes]
rs2497322	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497323	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497324	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497326	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497327	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497331	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497339	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[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497348	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497350	1.00[ASN][1000 genomes]
rs4517429	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933241	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933242	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933749	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933752	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583846	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583848	0.83[EUR][1000 genomes]
rs7069070	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7070025	0.88[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078376	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082382	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089179	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7477130	0.82[EUR][1000 genomes]
rs7893270	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894145	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897839	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7909191	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909581	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913340	0.84[CEU][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914859	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835250	0.82[EUR][1000 genomes]
rs860668	0.82[EUR][1000 genomes]
rs9419746	1.00[ASN][1000 genomes]
rs9633695	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973733	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980204	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041805	chr10:94624759-94699623	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv895898	chr10:94628274-94810665	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1039122	chr10:94636267-94693706	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1409387	EXOC6	cis	parietal	SCAN
rs1409387	CEP55	cis	cerebellum	SCAN
rs1409387	NOC3L	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:94620000-94657600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:94624400-94646000	Weak transcription	Fetal Intestine Small	intestine
3	chr10:94633200-94636400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr10:94633200-94640000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr10:94633200-94640200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr10:94633400-94636400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr10:94633400-94636600	Enhancers	HUVEC	blood vessel
8	chr10:94633400-94656600	Weak transcription	Primary B cells from cord blood	blood
9	chr10:94634800-94636800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:94634800-94650400	Weak transcription	Psoas Muscle	Psoas
11	chr10:94636000-94636400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:94636000-94637000	Enhancers	Adipose Nuclei	Adipose
13	chr10:94636000-94637200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr10:94636000-94637200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr10:94636000-94637400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr10:94636000-94637400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr10:94636000-94637400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr10:94636000-94637400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr10:94636000-94637400	Enhancers	Liver	Liver
20	chr10:94636000-94637600	Enhancers	Primary T cells from cord blood	blood
21	chr10:94636000-94638200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr10:94636000-94638400	Enhancers	Primary hematopoietic stem cells	blood
23	chr10:94636000-94638600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:94636000-94638600	Enhancers	K562	blood
25	chr10:94636000-94641000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:94636200-94636400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr10:94636200-94637000	Enhancers	Brain Hippocampus Middle	brain
28	chr10:94636200-94637000	Enhancers	A549	lung
29	chr10:94636200-94637200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr10:94636200-94637400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr10:94636200-94639200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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