Variant report

Variant	rs12380573
Chromosome Location	chr9:71361827-71361828
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:71361257..71364169-chr9:71367076..71369811,4	K562	blood:
2	chr9:71317976..71320955-chr9:71361746..71363959,2	K562	blood:
3	chr9:71345141..71347064-chr9:71360683..71362254,2	K562	blood:
4	chr9:71354907..71358283-chr9:71360291..71362317,4	MCF-7	breast:
5	chr9:71361634..71364182-chr9:71379350..71381885,2	K562	blood:
6	chr9:71360620..71364939-chr9:71391141..71394857,5	K562	blood:
7	chr9:71360686..71364939-chr9:71391201..71394992,4	K562	blood:
8	chr9:71361632..71363163-chr9:71392966..71395444,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000187866	Chromatin interaction
ENSG00000107242	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10116755	0.87[GIH][hapmap]
rs10125301	0.87[GIH][hapmap]
rs10869249	0.87[GIH][hapmap]
rs10869320	1.00[MEX][hapmap]
rs10869538	0.82[MEX][hapmap]
rs11143558	0.87[GIH][hapmap]
rs11143691	0.82[MEX][hapmap]
rs11143761	1.00[MEX][hapmap]
rs11143951	1.00[MEX][hapmap]
rs11144059	0.82[MEX][hapmap]
rs11144136	1.00[MEX][hapmap]
rs11144178	1.00[MEX][hapmap]
rs11144206	1.00[MEX][hapmap]
rs11144305	1.00[MEX][hapmap]
rs11144351	1.00[MEX][hapmap]
rs12003432	0.82[MEX][hapmap]
rs12340186	0.84[ASN][1000 genomes]
rs12379662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552102	0.82[MEX][hapmap]
rs12555728	0.82[MEX][hapmap]
rs1414954	1.00[MEX][hapmap]
rs17058792	0.82[MEX][hapmap]
rs17391456	1.00[MEX][hapmap]
rs28704681	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45501692	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623507	0.82[MEX][hapmap]
rs7865397	1.00[MEX][hapmap]
rs950786	0.82[MEX][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	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893415	chr9:71347988-71364351	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12380573	PTAR1	cis	parietal	SCAN
rs12380573	FAM189A2	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71343400-71363000	Weak transcription	GM12878-XiMat	blood
2	chr9:71351000-71370600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:71352400-71365800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:71355000-71362000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr9:71355000-71364400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:71355000-71365400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:71355600-71364200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr9:71356200-71362400	Genic enhancers	Fetal Intestine Small	intestine
9	chr9:71356200-71364800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:71356800-71362800	Weak transcription	Small Intestine	intestine
11	chr9:71357200-71363400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr9:71357800-71362600	Strong transcription	Primary B cells from cord blood	blood
13	chr9:71358800-71362400	Enhancers	Fetal Heart	heart
14	chr9:71359800-71362800	Enhancers	Stomach Mucosa	stomach
15	chr9:71360000-71370600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:71360200-71365400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:71360200-71370600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:71360600-71364000	Weak transcription	HepG2	liver
19	chr9:71361200-71362000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:71361200-71362200	Enhancers	Left Ventricle	heart
21	chr9:71361200-71362400	Enhancers	Placenta	Placenta
22	chr9:71361200-71363200	Enhancers	Fetal Intestine Large	intestine
23	chr9:71361400-71362200	Enhancers	Gastric	stomach
24	chr9:71361400-71362200	Enhancers	Pancreas	Pancrea
25	chr9:71361400-71362200	Enhancers	Right Ventricle	heart
26	chr9:71361400-71362200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:71361400-71362400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr9:71361400-71362600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:71361400-71363200	Enhancers	Brain Germinal Matrix	brain
30	chr9:71361400-71363400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr9:71361600-71362000	Enhancers	Primary hematopoietic stem cells	blood
32	chr9:71361600-71362000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr9:71361600-71362000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr9:71361600-71362000	Enhancers	Lung	lung
35	chr9:71361600-71362000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr9:71361600-71362000	Enhancers	Rectal Smooth Muscle	rectum
37	chr9:71361600-71362200	Enhancers	Colonic Mucosa	Colon
38	chr9:71361600-71362200	Enhancers	Right Atrium	heart
39	chr9:71361600-71362200	Flanking Active TSS	K562	blood
40	chr9:71361600-71362400	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr9:71361600-71364400	Weak transcription	Brain Angular Gyrus	brain
42	chr9:71361800-71362000	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr9:71361800-71362000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr9:71361800-71362200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:71361800-71362400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:71361800-71362400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:71361800-71362400	Flanking Active TSS	NHEK	skin

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