Variant report

Variant	rs3780346
Chromosome Location	chr9:94974188-94974189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94907454..94909829-chr9:94972993..94975829,2	MCF-7	breast:
2	chr9:94966366..94969198-chr9:94971038..94974978,3	MCF-7	breast:
3	chr9:94972713..94975511-chr9:94995305..94997135,2	K562	blood:
4	chr9:94972017..94974582-chr9:94993270..94995792,2	K562	blood:

Variant related genes	Relation type
ENSG00000238996	Chromatin interaction
ENSG00000236115	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10761149	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]
rs10761152	0.88[EUR][1000 genomes]
rs10761156	1.00[ASW][hapmap];0.88[CEU][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10820950	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10820951	0.81[EUR][1000 genomes]
rs10820952	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1152757	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1152759	0.89[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs1175788	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12552866	0.81[EUR][1000 genomes]
rs1760318	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1923599	0.82[CEU][hapmap]
rs2025389	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2031262	1.00[ASW][hapmap];0.89[CEU][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2147060	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2398751	0.84[EUR][1000 genomes]
rs3174352	0.82[EUR][1000 genomes]
rs3736835	0.85[CEU][hapmap]
rs3996311	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs471478	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4743869	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4744126	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs504708	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6479417	1.00[YRI][hapmap]
rs6651532	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7040860	0.81[EUR][1000 genomes]
rs710163	0.85[CEU][hapmap]
rs7467899	0.80[EUR][1000 genomes]
rs9299402	0.80[EUR][1000 genomes]
rs9409664	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9409667	0.85[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3780346	ZNF484	cis	cerebellum	SCAN
rs3780346	OMD	cis	cerebellum	SCAN
rs3780346	SPTLC1	cis	parietal	SCAN
rs3780346	ZNF484	cis	parietal	SCAN
rs3780346	CENPP	cis	parietal	SCAN
rs3780346	CENPP	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94968800-94976800	Strong transcription	A549	lung
2	chr9:94969000-94975400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:94969600-94975000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:94969600-94976200	Strong transcription	NH-A	brain
5	chr9:94969600-94977000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:94969800-94975400	Strong transcription	Osteobl	bone
7	chr9:94969800-94976400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:94969800-94976800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:94970000-94976600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:94970200-94974200	Strong transcription	Left Ventricle	heart
11	chr9:94970400-94975000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:94970400-94976000	Strong transcription	Hela-S3	cervix
13	chr9:94970400-94976400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr9:94970400-94976600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:94970400-94976600	Strong transcription	Liver	Liver
16	chr9:94970400-94976600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr9:94970400-94976800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:94970400-94976800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:94970400-94977200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:94970400-94977800	Strong transcription	Primary T cells from cord blood	blood
21	chr9:94970600-94976400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr9:94970600-94976400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:94970600-94976400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:94970600-94976400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:94970600-94976600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:94970600-94976600	Strong transcription	HMEC	breast
27	chr9:94970800-94975000	Strong transcription	Psoas Muscle	Psoas
28	chr9:94970800-94975200	Strong transcription	NHDF-Ad	bronchial
29	chr9:94970800-94975400	Strong transcription	Adipose Nuclei	Adipose
30	chr9:94970800-94975400	Strong transcription	NHLF	lung
31	chr9:94970800-94976000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:94970800-94976000	Strong transcription	HSMMtube	muscle
33	chr9:94970800-94976200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr9:94970800-94976400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr9:94970800-94976400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:94970800-94976400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr9:94970800-94976400	Strong transcription	Brain Substantia Nigra	brain
38	chr9:94970800-94976600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:94970800-94976600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:94970800-94976600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:94970800-94976600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:94970800-94976600	Strong transcription	Brain Germinal Matrix	brain
43	chr9:94970800-94976600	Strong transcription	Brain Hippocampus Middle	brain
44	chr9:94970800-94976600	Strong transcription	Fetal Thymus	thymus
45	chr9:94970800-94976600	Strong transcription	Dnd41	blood
46	chr9:94970800-94976800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:94970800-94976800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr9:94970800-94976800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:94970800-94976800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:94970800-94976800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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