Variant report

Variant	rs10817474
Chromosome Location	chr9:116040440-116040441
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116038235..116040898-chr9:116423469..116425169,2	MCF-7	breast:
2	chr9:115512698..115514461-chr9:116038293..116041061,2	MCF-7	breast:
3	chr9:116033413..116040476-chr9:116169994..116174441,15	MCF-7	breast:
4	chr9:116038438..116040494-chr9:116158946..116160891,2	MCF-7	breast:
5	chr9:116039888..116041521-chr9:116060320..116062417,2	K562	blood:

Variant related genes	Relation type
ENSG00000148158	Chromatin interaction
ENSG00000226609	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000148218	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10117451	0.80[ASN][1000 genomes]
rs10123780	0.86[CEU][hapmap]
rs10759638	0.86[CEU][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817475	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981712	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10981715	0.86[CEU][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10981720	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10981723	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs11552582	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11789755	0.86[CEU][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs12337498	0.86[CEU][hapmap]
rs12343629	0.86[CEU][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17764013	0.86[CEU][hapmap];1.00[YRI][hapmap]
rs2296073	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs3087548	0.86[CEU][hapmap]
rs3750532	0.90[CEU][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs3750533	0.86[CEU][hapmap];0.80[JPT][hapmap]
rs3750534	0.86[CEU][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3750535	0.86[CEU][hapmap]
rs3810917	0.86[CEU][hapmap]
rs3810918	0.86[CEU][hapmap]
rs3810919	0.86[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4979231	0.86[CEU][hapmap];0.80[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4979232	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979233	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6478000	0.81[EUR][1000 genomes]
rs7032466	0.81[LWK][hapmap]
rs7847295	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9299214	0.86[CEU][hapmap]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10817474	CDC26	cis	parietal	SCAN
rs10817474	CDC26	cis	Whole Blood	GTEx
rs10817474	CDC26	cis	Esophagus Mucosa	GTEx
rs10817474	PRPF4	cis	Thyroid	GTEx
rs10817474	ZNF483	cis	cerebellum	SCAN
rs10817474	CDC26	cis	Thyroid	GTEx
rs10817474	CDC26	cis	lung	GTEx
rs10817474	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs10817474	CDC26	cis	Heart Left Ventricle	GTEx
rs10817474	CDC26	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116038400-116041200	Weak transcription	Gastric	stomach
2	chr9:116038600-116041200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:116038600-116042200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:116038600-116050400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:116038800-116041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:116038800-116041200	Weak transcription	Aorta	Aorta
7	chr9:116038800-116041200	Weak transcription	Left Ventricle	heart
8	chr9:116038800-116041200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:116038800-116041800	Weak transcription	Fetal Kidney	kidney
10	chr9:116038800-116041800	Weak transcription	Small Intestine	intestine
11	chr9:116038800-116048400	Weak transcription	Stomach Mucosa	stomach
12	chr9:116038800-116060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:116039000-116040600	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:116039000-116040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:116039000-116040600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:116039000-116040600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:116039000-116040600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:116039000-116040600	Weak transcription	NHLF	lung
19	chr9:116039000-116040800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:116039000-116040800	Weak transcription	Brain Substantia Nigra	brain
21	chr9:116039000-116040800	Enhancers	Fetal Brain Female	brain
22	chr9:116039000-116040800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:116039000-116041000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:116039000-116041000	Weak transcription	Brain Anterior Caudate	brain
25	chr9:116039000-116041000	Weak transcription	Fetal Intestine Large	intestine
26	chr9:116039000-116041200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr9:116039000-116041200	Weak transcription	Esophagus	oesophagus
28	chr9:116039000-116041200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:116039000-116041200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:116039000-116041200	Weak transcription	Thymus	Thymus
31	chr9:116039000-116041200	Genic enhancers	Dnd41	blood
32	chr9:116039000-116041800	Weak transcription	Psoas Muscle	Psoas
33	chr9:116039000-116041800	Weak transcription	Spleen	Spleen
34	chr9:116039000-116042000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:116039000-116042000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:116039000-116042000	Weak transcription	Brain Angular Gyrus	brain
37	chr9:116039000-116042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:116039000-116042000	Weak transcription	Right Ventricle	heart
39	chr9:116039000-116042200	Weak transcription	Ovary	ovary
40	chr9:116039000-116042200	Weak transcription	Pancreas	Pancrea
41	chr9:116039000-116042200	Weak transcription	NHDF-Ad	bronchial
42	chr9:116039000-116043400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:116039000-116043400	Weak transcription	Colonic Mucosa	Colon
44	chr9:116039000-116056800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:116039000-116058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:116039200-116040600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr9:116039200-116040800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:116039200-116040800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr9:116039200-116040800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr9:116039200-116041000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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