Variant report

Variant	rs11172139
Chromosome Location	chr12:57656705-57656706
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57655062..57656842-chr12:57848026..57849924,2	K562	blood:
2	chr12:57654094..57657253-chr12:57855291..57857912,3	K562	blood:
3	chr12:57655342..57658281-chr12:57847434..57849924,2	K562	blood:

Variant related genes	Relation type
ENSG00000111087	Chromatin interaction
ENSG00000139269	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11172145	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11172152	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11172161	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11172163	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172166	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs11172176	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes]
rs11172184	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs12371805	0.95[ASN][1000 genomes]
rs34095989	1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs34453452	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap]
rs34537746	0.84[AMR][1000 genomes]
rs35058761	0.83[AMR][1000 genomes]
rs6581140	0.83[AMR][1000 genomes]
rs7133915	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7139302	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7486863	0.82[AMR][1000 genomes]
rs7975026	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7975634	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11172139	DKFZP586D0919	cis	multi-tissue	Pritchard
rs11172139	ZNF385A	cis	parietal	SCAN
rs11172139	OR6C4	cis	parietal	SCAN
rs11172139	SILV	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57638800-57673600	Weak transcription	Stomach Mucosa	stomach
2	chr12:57646000-57667600	Strong transcription	Thymus	Thymus
3	chr12:57646200-57657000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:57647000-57657000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:57647000-57657200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:57647200-57657000	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr12:57647200-57657200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:57647200-57657200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:57647200-57657400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:57647200-57657800	Strong transcription	Fetal Thymus	thymus
11	chr12:57647200-57668200	Strong transcription	Fetal Stomach	stomach
12	chr12:57648000-57657200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:57648000-57657200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:57648000-57657400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:57648000-57657400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:57648200-57657400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr12:57648200-57657400	Strong transcription	Primary T cells from cord blood	blood
18	chr12:57648400-57656800	Strong transcription	Primary B cells from cord blood	blood
19	chr12:57648400-57656800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:57648400-57656800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:57648400-57656800	Strong transcription	NHLF	lung
22	chr12:57648400-57657000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:57648400-57657000	Strong transcription	Adipose Nuclei	Adipose
24	chr12:57648400-57657000	Strong transcription	Colon Smooth Muscle	Colon
25	chr12:57648400-57657200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:57648400-57657200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:57648400-57657200	Strong transcription	Fetal Intestine Large	intestine
28	chr12:57648400-57657200	Strong transcription	Placenta	Placenta
29	chr12:57648400-57661600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:57648600-57656800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:57648600-57657200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:57648800-57657000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:57649200-57656800	Strong transcription	Fetal Lung	lung
34	chr12:57651200-57656800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr12:57651200-57657200	Strong transcription	NHDF-Ad	bronchial
36	chr12:57652000-57662000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:57652000-57662000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:57652000-57673600	Weak transcription	Hela-S3	cervix
39	chr12:57652200-57658600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:57652600-57657400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr12:57652600-57658800	Enhancers	Psoas Muscle	Psoas
42	chr12:57653000-57657600	Weak transcription	GM12878-XiMat	blood
43	chr12:57653200-57659600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr12:57653200-57660600	Weak transcription	HUVEC	blood vessel
45	chr12:57653200-57666800	Weak transcription	HMEC	breast
46	chr12:57653400-57671400	Weak transcription	Small Intestine	intestine
47	chr12:57653600-57658600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:57653800-57657000	Enhancers	Fetal Heart	heart
49	chr12:57653800-57657200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:57653800-57657200	Strong transcription	Osteobl	bone

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