Variant report

Variant	rs10819320
Chromosome Location	chr9:101571655-101571656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101570471..101572096-chr9:101573818..101575342,2	K562	blood:
2	chr9:101570786..101573911-chr9:101592967..101596373,4	K562	blood:
3	chr9:101571158..101574064-chr9:101576391..101578581,2	K562	blood:
4	chr9:101569719..101571295-chr9:101571533..101573383,2	MCF-7	breast:
5	chr9:101556573..101560424-chr9:101566029..101574080,12	MCF-7	breast:
6	chr9:101571611..101574366-chr9:101836561..101838250,2	K562	blood:
7	chr9:101567600..101569220-chr9:101571487..101573916,3	MCF-7	breast:
8	chr9:101571350..101572921-chr9:101580926..101583475,2	K562	blood:
9	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:
10	chr9:101570706..101573424-chr9:101594873..101597153,4	K562	blood:
11	chr9:101570653..101573493-chr9:101866236..101867897,2	K562	blood:
12	chr9:101555483..101562112-chr9:101568669..101573087,9	K562	blood:
13	chr9:101570303..101574512-chr9:101580563..101586059,9	K562	blood:
14	chr9:101557242..101560519-chr9:101566443..101572716,8	MCF-7	breast:
15	chr9:101571089..101573557-chr9:101759747..101761480,2	MCF-7	breast:
16	chr9:101543983..101545849-chr9:101571655..101573219,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000119514	Chromatin interaction
ENSG00000106799	Chromatin interaction
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10121153	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1022796	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739690	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10760475	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10760479	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10760494	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10819266	0.84[ASN][1000 genomes]
rs10819308	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10987747	0.89[ASW][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs10987749	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10987771	0.89[EUR][1000 genomes]
rs10987794	0.84[EUR][1000 genomes]
rs11791440	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12056975	0.82[EUR][1000 genomes]
rs1543506	0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs1555519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2146255	0.89[EUR][1000 genomes]
rs33998698	0.89[EUR][1000 genomes]
rs3933477	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742737	0.90[ASN][1000 genomes]
rs4742738	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs4742741	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs4742745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743282	0.90[ASN][1000 genomes]
rs6478839	0.88[ASN][1000 genomes]
rs6478845	0.87[ASN][1000 genomes]
rs7018907	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7020056	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7027405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7038640	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7047722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7357783	0.90[ASN][1000 genomes]
rs7469116	0.90[ASN][1000 genomes]
rs7853904	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7861186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7865233	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9886821	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10819320	C9orf130	cis	cerebellum	SCAN
rs10819320	ZNF189	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101570400-101572200	Weak transcription	HSMMtube	muscle
2	chr9:101570600-101572000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
3	chr9:101570600-101572200	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr9:101570600-101573000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:101570600-101573200	Flanking Active TSS	K562	blood
6	chr9:101570800-101571800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr9:101570800-101572000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr9:101570800-101572000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:101570800-101572000	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr9:101570800-101572200	Weak transcription	HSMM	muscle
11	chr9:101570800-101572600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr9:101571000-101571800	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr9:101571000-101571800	Bivalent/Poised TSS	Fetal Stomach	stomach
14	chr9:101571000-101572000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr9:101571000-101572000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
16	chr9:101571000-101572000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr9:101571000-101572200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:101571000-101572200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:101571000-101572200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr9:101571000-101572600	Enhancers	Pancreas	Pancrea
21	chr9:101571000-101572600	Weak transcription	A549	lung
22	chr9:101571000-101574000	Enhancers	NHEK	skin
23	chr9:101571000-101586600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:101571200-101571800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:101571200-101571800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:101571200-101572000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr9:101571200-101572200	Weak transcription	Right Atrium	heart
28	chr9:101571200-101572200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
29	chr9:101571200-101572400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:101571200-101572400	Weak transcription	Primary T cells from cord blood	blood
31	chr9:101571200-101572400	Enhancers	Colon Smooth Muscle	Colon
32	chr9:101571200-101572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:101571200-101572800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr9:101571200-101572800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr9:101571200-101573000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:101571200-101573800	Enhancers	Fetal Intestine Large	intestine
37	chr9:101571200-101574000	Enhancers	NHDF-Ad	bronchial
38	chr9:101571200-101574000	Enhancers	NHLF	lung
39	chr9:101571200-101577000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:101571400-101571800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:101571400-101571800	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr9:101571400-101572400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:101571400-101572400	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr9:101571400-101573000	Enhancers	Esophagus	oesophagus
45	chr9:101571600-101571800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr9:101571600-101572200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:101571600-101572200	Weak transcription	Gastric	stomach
48	chr9:101571600-101572400	Enhancers	Colonic Mucosa	Colon
49	chr9:101571600-101572400	Enhancers	Fetal Lung	lung
50	chr9:101571600-101572400	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links