Variant report

Variant	rs331380
Chromosome Location	chr9:95256519-95256520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95227770..95231627-chr9:95254593..95257141,3	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10283572	0.83[JPT][hapmap]
rs10453241	0.81[JPT][hapmap]
rs10491806	1.00[YRI][hapmap]
rs1053446	0.81[JPT][hapmap]
rs10761154	0.84[JPT][hapmap]
rs10761156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10761158	0.81[JPT][hapmap]
rs10820969	0.81[JPT][hapmap]
rs10820971	0.81[JPT][hapmap]
rs10820998	1.00[YRI][hapmap]
rs10992322	0.81[JPT][hapmap]
rs10992347	0.81[JPT][hapmap]
rs10992367	1.00[YRI][hapmap]
rs10992380	1.00[YRI][hapmap]
rs10992407	1.00[YRI][hapmap]
rs1152757	0.81[EUR][1000 genomes]
rs1152759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1175788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1323523	1.00[YRI][hapmap]
rs1535754	0.81[JPT][hapmap]
rs1853468	1.00[YRI][hapmap]
rs1923599	0.93[CEU][hapmap]
rs1924243	0.81[JPT][hapmap]
rs2025388	0.81[JPT][hapmap]
rs2025389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2031262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131919	1.00[YRI][hapmap]
rs2147060	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs2181712	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274966	0.81[JPT][hapmap]
rs230222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398751	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2516567	0.81[JPT][hapmap]
rs3174352	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs331377	0.93[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs331379	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs331381	0.93[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs3996311	0.81[EUR][1000 genomes]
rs4743869	0.81[EUR][1000 genomes]
rs4744126	0.81[EUR][1000 genomes]
rs4744133	0.81[JPT][hapmap]
rs504708	0.81[EUR][1000 genomes]
rs6479417	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs6479419	0.81[JPT][hapmap]
rs7020874	0.81[JPT][hapmap]
rs7022562	0.81[JPT][hapmap]
rs7023004	0.81[JPT][hapmap]
rs7026361	0.81[JPT][hapmap]
rs7037075	0.81[JPT][hapmap]
rs7037194	0.81[JPT][hapmap]
rs7045409	0.81[JPT][hapmap]
rs7047089	0.81[JPT][hapmap]
rs710162	0.81[JPT][hapmap]
rs710163	0.89[CEU][hapmap];0.81[TSI][hapmap]
rs7467899	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7847929	0.81[JPT][hapmap]
rs7850432	0.81[JPT][hapmap]
rs7853859	0.81[JPT][hapmap]
rs7856147	1.00[YRI][hapmap]
rs7857502	1.00[YRI][hapmap]
rs7867300	1.00[CEU][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7872375	0.81[JPT][hapmap]
rs912264	1.00[YRI][hapmap]
rs9299404	0.81[JPT][hapmap]
rs9409664	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9409667	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs971984	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1049599	chr9:95170139-95265558	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv1822933	chr9:95255176-95293308	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs331380	FBP1	cis	parietal	SCAN
rs331380	ZNF484	cis	parietal	SCAN
rs331380	FANCC	cis	cerebellum	SCAN
rs331380	ECM2	cis	cerebellum	SCAN
rs331380	CENPP	cis	cerebellum	SCAN
rs331380	CENPP	cis	parietal	SCAN
rs331380	ZNF484	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95231800-95268800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:95243600-95263800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:95246200-95261200	Weak transcription	Right Atrium	heart
4	chr9:95246400-95267000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:95249400-95256800	Enhancers	Fetal Stomach	stomach
6	chr9:95252200-95256600	Weak transcription	Psoas Muscle	Psoas
7	chr9:95252200-95258000	Weak transcription	NHDF-Ad	bronchial
8	chr9:95252200-95258400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:95252200-95263800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:95252200-95266400	Weak transcription	NHLF	lung
11	chr9:95252400-95258600	Weak transcription	HSMM	muscle
12	chr9:95252400-95261200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:95252400-95266200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:95252600-95269400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:95254000-95256600	Enhancers	Rectal Smooth Muscle	rectum
16	chr9:95254800-95258000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:95255000-95256800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:95255000-95274600	Weak transcription	Liver	Liver
19	chr9:95255200-95263200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:95255200-95264000	Weak transcription	Esophagus	oesophagus
21	chr9:95255400-95257200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:95255400-95258800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:95255400-95263200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:95255400-95263800	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:95255400-95264000	Weak transcription	Aorta	Aorta
26	chr9:95255400-95266600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr9:95255400-95269400	Weak transcription	Right Ventricle	heart
28	chr9:95255600-95258600	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:95255600-95260200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:95256200-95256600	Genic enhancers	Fetal Lung	lung
31	chr9:95256200-95256600	Strong transcription	Ovary	ovary
32	chr9:95256200-95257400	Strong transcription	Adipose Nuclei	Adipose
33	chr9:95256200-95257600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:95256200-95264200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:95256400-95258600	Enhancers	Fetal Heart	heart

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