Variant report

Variant	rs1417738
Chromosome Location	chr9:102569599-102569600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102569326..102570227-chr9:102773024..102773804,2	MCF-7	breast:
2	chr9:102568407..102574196-chr9:102578455..102584967,12	MCF-7	breast:
3	chr9:102568705..102572771-chr9:102577522..102579718,3	MCF-7	breast:
4	chr9:102568851..102571702-chr9:102571875..102575192,3	MCF-7	breast:
5	chr9:102569567..102571889-chr9:102580660..102583894,3	MCF-7	breast:
6	chr9:102569282..102569953-chr9:102773070..102773862,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119508	Chromatin interaction
ENSG00000237461	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10156557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988895	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988904	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988905	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336436	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1405209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918734	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918009	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965564	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900222	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742773	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742774	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029559	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038780	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041475	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047636	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744685	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7467433	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893621	chr9:102342950-102585545	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv528025	chr9:102540386-102613672	Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv893622	chr9:102543355-102595685	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1417738	C9orf125	cis	parietal	SCAN
rs1417738	PPP3R2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102547600-102573400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:102555400-102577200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:102555600-102572200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:102557400-102581400	Weak transcription	Pancreas	Pancrea
5	chr9:102559800-102581600	Weak transcription	Gastric	stomach
6	chr9:102560000-102580600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:102560400-102571800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:102560400-102580800	Weak transcription	Fetal Stomach	stomach
9	chr9:102560800-102570200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:102561200-102569800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:102561200-102573400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:102561200-102573400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:102561200-102580800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:102561400-102570000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:102561600-102573600	Weak transcription	Aorta	Aorta
16	chr9:102562800-102572400	Weak transcription	Fetal Lung	lung
17	chr9:102562800-102580800	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:102562800-102580800	Weak transcription	HSMMtube	muscle
19	chr9:102563000-102569800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:102563800-102577400	Weak transcription	Fetal Heart	heart
21	chr9:102564200-102570200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:102564400-102577400	Weak transcription	Psoas Muscle	Psoas
23	chr9:102564400-102580000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:102564400-102581400	Weak transcription	Ovary	ovary
25	chr9:102564600-102573200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:102565200-102571800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:102565600-102569800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr9:102565800-102569800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:102566000-102572000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:102566000-102580800	Weak transcription	Left Ventricle	heart
31	chr9:102566400-102572000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:102566400-102572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:102566600-102580800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:102567000-102570200	Weak transcription	Brain Angular Gyrus	brain
35	chr9:102567000-102573200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:102567200-102569800	Weak transcription	GM12878-XiMat	blood
37	chr9:102567200-102576800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:102567400-102581600	Weak transcription	Lung	lung
39	chr9:102567800-102571400	Weak transcription	Primary B cells from cord blood	blood
40	chr9:102569400-102569800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr9:102569400-102569800	Weak transcription	NHLF	lung
42	chr9:102569400-102570000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr9:102569400-102570000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr9:102569400-102570000	Enhancers	Brain Substantia Nigra	brain
45	chr9:102569400-102570000	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr9:102569400-102570000	Enhancers	Rectal Smooth Muscle	rectum

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