Variant report

Variant	rs10761149
Chromosome Location	chr9:94988945-94988946
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	chr9:94987548..94989488-chr9:94989589..94991476,2	MCF-7	breast:
2	chr9:94987677..94991575-chr9:94991944..94994722,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10156482	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10761152	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761156	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10820950	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10820951	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10820952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1152757	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[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1152759	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1175788	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12552866	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1760318	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1923599	0.89[CEU][hapmap]
rs1960094	0.87[ASN][1000 genomes]
rs2025389	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2031262	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2147060	0.96[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs2181712	0.83[EUR][1000 genomes]
rs2398751	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3174352	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3736835	0.92[CEU][hapmap]
rs3780346	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3847317	0.81[ASN][1000 genomes]
rs3996311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471478	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];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744121	0.81[ASN][1000 genomes]
rs4744122	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs4744126	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504708	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479417	1.00[YRI][hapmap]
rs6651532	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[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028854	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs7040860	0.88[EUR][1000 genomes]
rs710163	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs7467899	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7867300	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs9299402	0.89[EUR][1000 genomes]
rs9409664	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[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409667	0.94[EUR][1000 genomes];0.96[ASN][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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10761149	ECM2	cis	cerebellum	SCAN
rs10761149	CENPP	cis	cerebellum	SCAN
rs10761149	OGN	cis	Nerve Tibial	GTEx
rs10761149	ZNF484	cis	cerebellum	SCAN
rs10761149	ZNF484	cis	parietal	SCAN
rs10761149	SPTLC1	cis	parietal	SCAN
rs10761149	FANCC	cis	cerebellum	SCAN
rs10761149	FBP1	cis	parietal	SCAN
rs10761149	CENPP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94973800-94990400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:94974000-94999000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:94982800-94989000	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:94982800-94989000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:94982800-94989000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:94982800-94989000	Strong transcription	Primary T cells from cord blood	blood
7	chr9:94982800-94989000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr9:94982800-94989000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr9:94982800-94989000	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:94982800-94989000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr9:94982800-94989000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:94982800-94989000	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr9:94982800-94989000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:94982800-94989000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:94982800-94989000	Strong transcription	Brain Angular Gyrus	brain
16	chr9:94982800-94989000	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr9:94982800-94989000	Strong transcription	Fetal Brain Female	brain
18	chr9:94982800-94989000	Strong transcription	Placenta	Placenta
19	chr9:94982800-94989000	Strong transcription	Gastric	stomach
20	chr9:94982800-94989000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr9:94982800-94989000	Strong transcription	Rectal Smooth Muscle	rectum
22	chr9:94982800-94989000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:94982800-94989000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr9:94982800-94989000	Strong transcription	Dnd41	blood
25	chr9:94982800-94989000	Strong transcription	Hela-S3	cervix
26	chr9:94982800-94989000	Strong transcription	HSMMtube	muscle
27	chr9:94982800-94989000	Strong transcription	HUVEC	blood vessel
28	chr9:94982800-94989000	Strong transcription	K562	blood
29	chr9:94982800-94989000	Strong transcription	NHEK	skin
30	chr9:94982800-94989000	Strong transcription	Osteobl	bone
31	chr9:94982800-94989200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:94982800-94989200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:94982800-94989200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:94982800-94989200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:94982800-94989200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr9:94982800-94989200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:94982800-94989200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr9:94982800-94989200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:94982800-94989200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:94982800-94989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:94982800-94989200	Strong transcription	Left Ventricle	heart
42	chr9:94982800-94989200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr9:94982800-94989400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr9:94982800-94989400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:94982800-94989400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:94982800-94989400	Strong transcription	Fetal Intestine Large	intestine
47	chr9:94982800-94989400	Strong transcription	Fetal Thymus	thymus
48	chr9:94982800-94989400	Strong transcription	HepG2	liver
49	chr9:94982800-94990800	Strong transcription	Liver	Liver
50	chr9:94982800-94990800	Strong transcription	Ovary	ovary

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