Variant report

Variant	rs12004883
Chromosome Location	chr9:110006333-110006334
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:110004629..110007184-chr9:110036620..110038464,2	MCF-7	breast:
2	chr9:110000595..110013733-chr9:110042800..110048700,27	MCF-7	breast:
3	chr9:110004582..110011651-chr9:110041707..110048879,25	MCF-7	breast:
4	chr9:109972512..109975127-chr9:110005713..110007836,2	MCF-7	breast:
5	chr9:109893618..109894481-chr9:110005806..110006859,6	MCF-7	breast:
6	chr9:109999870..110001713-chr9:110004205..110007979,4	K562	blood:
7	chr9:110005542..110008121-chr9:110058915..110061761,2	MCF-7	breast:
8	chr9:109893940..109894573-chr9:110005787..110006748,4	MCF-7	breast:
9	chr9:110005830..110006352-chr9:110046858..110047394,2	MCF-7	breast:
10	chr9:109893966..109894573-chr9:110005787..110006671,2	MCF-7	breast:
11	chr9:109998399..110000270-chr9:110004881..110006442,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10978789	1.00[CHB][hapmap]
rs10978793	1.00[CHB][hapmap]
rs11573631	1.00[CHB][hapmap]
rs11573652	1.00[CHB][hapmap]
rs11573655	1.00[CHB][hapmap]
rs11573700	1.00[CHB][hapmap]
rs11790702	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793153	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794742	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004743	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004782	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005522	1.00[CHB][hapmap]
rs13287718	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16912372	1.00[CHB][hapmap]
rs34181494	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34443778	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35035115	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35062164	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35188506	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35389266	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622672	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36116755	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60819822	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859324	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893698	chr9:109998563-110052660	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12004883	NIPSNAP3B	cis	cerebellum	SCAN
rs12004883	C9orf5	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109998600-110006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:109999200-110008600	Weak transcription	Liver	Liver
3	chr9:110002000-110010000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:110002000-110011400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:110002400-110011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:110002400-110011200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:110002800-110010200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:110003400-110010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:110003600-110010800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:110004000-110006400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:110004200-110008000	Weak transcription	Fetal Kidney	kidney
12	chr9:110004200-110011200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:110004600-110006600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr9:110004800-110006400	Enhancers	HSMM	muscle
15	chr9:110004800-110006600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr9:110004800-110006800	Enhancers	Hela-S3	cervix
17	chr9:110004800-110007200	Enhancers	HMEC	breast
18	chr9:110004800-110007200	Enhancers	NHEK	skin
19	chr9:110005000-110006400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr9:110005000-110006400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:110005000-110006600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:110005000-110006600	Enhancers	NH-A	brain
23	chr9:110005000-110007000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr9:110005200-110006400	Enhancers	NHDF-Ad	bronchial
25	chr9:110005400-110010000	Weak transcription	HSMMtube	muscle
26	chr9:110005600-110006600	Enhancers	Fetal Intestine Large	intestine
27	chr9:110005600-110006800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr9:110005600-110006800	Enhancers	HepG2	liver
29	chr9:110005800-110006400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr9:110005800-110006400	Enhancers	Psoas Muscle	Psoas
31	chr9:110005800-110006400	Enhancers	Osteobl	bone
32	chr9:110005800-110006600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr9:110005800-110006600	Enhancers	Fetal Intestine Small	intestine
34	chr9:110005800-110006600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr9:110006000-110006400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:110006000-110006400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr9:110006000-110006400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:110006000-110006400	Enhancers	NHLF	lung
39	chr9:110006000-110006600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr9:110006000-110006600	Flanking Active TSS	A549	lung
41	chr9:110006000-110006600	Enhancers	GM12878-XiMat	blood
42	chr9:110006000-110007800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:110006000-110011000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:110006200-110006400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:110006200-110006400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr9:110006200-110006600	Weak transcription	Placenta	Placenta
47	chr9:110006200-110007200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr9:110006200-110010800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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