Variant report

Variant	rs17109869
Chromosome Location	chr10:96000162-96000163
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	chr10:95999725..96001564-chr10:96001997..96003739,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10786156	0.84[ASW][hapmap]
rs11187830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12258052	1.00[MEX][hapmap]
rs1408820	0.80[CHD][hapmap];1.00[MEX][hapmap]
rs1830890	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1858610	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34775698	0.87[EUR][1000 genomes]
rs35443777	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3740362	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4917450	0.82[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4918172	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4918188	0.96[CEU][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55753709	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7072574	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7075045	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7919066	0.84[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7919320	0.82[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9787457	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9787670	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17109869	C10orf129	cis	cerebellum	SCAN
rs17109869	CYP2C18	cis	cerebellum	SCAN
rs17109869	NOC3L	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95970800-96005800	Weak transcription	Colonic Mucosa	Colon
2	chr10:95973400-96012200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:95974200-96034000	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:95984600-96000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:95984800-96023800	Weak transcription	Pancreas	Pancrea
6	chr10:95985800-96005800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:95985800-96033800	Weak transcription	Left Ventricle	heart
8	chr10:95986000-96011400	Weak transcription	Stomach Mucosa	stomach
9	chr10:95988200-96005600	Weak transcription	Fetal Brain Female	brain
10	chr10:95989400-96005800	Weak transcription	Ovary	ovary
11	chr10:95989400-96005800	Weak transcription	Spleen	Spleen
12	chr10:95994600-96005800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:95994600-96045400	Weak transcription	Lung	lung
14	chr10:95994800-96005800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:95995000-96005800	Weak transcription	Gastric	stomach
16	chr10:95995200-96005800	Weak transcription	HSMMtube	muscle
17	chr10:95995800-96005800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr10:95995800-96005800	Weak transcription	Adipose Nuclei	Adipose
19	chr10:95995800-96051800	Weak transcription	Fetal Kidney	kidney
20	chr10:95996000-96002000	Weak transcription	Fetal Intestine Small	intestine
21	chr10:95996000-96005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr10:95997800-96000400	Weak transcription	Fetal Lung	lung
23	chr10:95997800-96005600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:95997800-96005600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:95998000-96005800	Weak transcription	Aorta	Aorta
26	chr10:95998200-96000200	Strong transcription	Fetal Muscle Leg	muscle
27	chr10:95998600-96002800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr10:95999400-96002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:95999400-96005600	Weak transcription	A549	lung
30	chr10:95999600-96001800	Enhancers	Fetal Stomach	stomach
31	chr10:95999600-96002200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr10:95999800-96004200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:95999800-96004200	Weak transcription	Fetal Intestine Large	intestine
34	chr10:95999800-96005800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:96000000-96005800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr10:96000000-96005800	Weak transcription	Rectal Mucosa Donor 29	rectum

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