Variant report

Variant	rs7866250
Chromosome Location	chr9:71994522-71994523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71992876..71994758-chr9:72000665..72002258,2	MCF-7	breast:
2	chr9:71649254..71651788-chr9:71993811..71996699,2	MCF-7	breast:
3	chr9:71940098..71942516-chr9:71992469..71994657,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165060	Chromatin interaction
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10116389	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10746594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10746613	0.89[AFR][1000 genomes]
rs10780334	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10780360	0.92[JPT][hapmap]
rs10780361	0.92[JPT][hapmap]
rs10867414	0.85[EUR][1000 genomes]
rs10867423	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10867481	0.84[AFR][1000 genomes]
rs12379338	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1334312	0.94[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1761290	0.85[AFR][1000 genomes]
rs1812971	0.87[AFR][1000 genomes]
rs1929896	0.93[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2309431	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes]
rs2777866	0.87[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2777878	0.87[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2781521	0.87[CEU][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs2781522	0.87[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs2781527	0.88[AFR][1000 genomes]
rs35625426	0.85[AFR][1000 genomes]
rs3858105	0.94[CEU][hapmap]
rs3896424	0.82[AFR][1000 genomes]
rs3934600	0.87[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4237232	0.84[AFR][1000 genomes]
rs4237233	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4237234	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4483220	0.87[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs4484762	0.87[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs4503164	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4744886	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4744894	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62570234	0.82[AFR][1000 genomes]
rs6559488	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs6559489	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs6559498	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559512	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6559513	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6559527	0.81[CEU][hapmap];0.80[AFR][1000 genomes]
rs7019551	0.93[CEU][hapmap]
rs7043451	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs7044071	0.82[JPT][hapmap]
rs7046199	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7856778	0.87[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs9314682	0.82[AMR][1000 genomes];0.82[EUR][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	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7866250	C9orf57	cis	cerebellum	SCAN
rs7866250	KLF9	cis	cerebellum	SCAN
rs7866250	C18orf16	trans	cerebellum	SCAN
rs7866250	TJP2	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
3	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:71988800-71998600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
7	chr9:71989600-71997000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:71990600-72000200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:71992000-71995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:71992000-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:71992200-71997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:71992200-72001800	Weak transcription	Adipose Nuclei	Adipose
15	chr9:71992400-71999400	Weak transcription	Brain Angular Gyrus	brain
16	chr9:71992400-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:71992600-71995200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:71992600-71996000	Weak transcription	Right Atrium	heart
19	chr9:71992600-72000800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
22	chr9:71992800-71997200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:71992800-71997400	Enhancers	Fetal Muscle Leg	muscle
24	chr9:71992800-71998200	Weak transcription	Ovary	ovary
25	chr9:71992800-71998400	Weak transcription	Fetal Stomach	stomach
26	chr9:71992800-72000200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:71992800-72001400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:71993000-71997000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:71993600-71996000	Enhancers	HUVEC	blood vessel
31	chr9:71993600-71997200	Enhancers	Stomach Smooth Muscle	stomach
32	chr9:71993800-71994800	Enhancers	Gastric	stomach
33	chr9:71993800-71995000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:71993800-71995400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:71993800-71996200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:71994000-71994600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr9:71994000-71994600	Enhancers	NH-A	brain
38	chr9:71994000-71995200	Flanking Active TSS	HSMMtube	muscle
39	chr9:71994000-71995800	Enhancers	Placenta	Placenta
40	chr9:71994000-71996000	Enhancers	Fetal Heart	heart
41	chr9:71994000-71997400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:71994000-71997400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:71994200-71994600	Flanking Active TSS	Right Ventricle	heart
44	chr9:71994200-71994800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:71994200-71994800	Enhancers	Lung	lung
46	chr9:71994200-71995000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr9:71994200-71995000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:71994200-71995000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:71994200-71995000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:71994200-71995000	Enhancers	Aorta	Aorta

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