Variant report

Variant	rs12140172
Chromosome Location	chr1:209549247-209549248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209547762..209552825-chr1:209601391..209605097,6	MCF-7	breast:
2	chr1:209547752..209549329-chr1:209603815..209605769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12064516	0.84[EUR][1000 genomes]
rs12116965	0.85[EUR][1000 genomes]
rs12119349	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119464	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12120032	0.88[EUR][1000 genomes]
rs12120757	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12121931	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12124710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12125098	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12125358	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126305	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12126769	0.90[EUR][1000 genomes]
rs12128640	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12135244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12137788	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12139847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140436	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144443	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12144663	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12144725	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12145008	0.90[EUR][1000 genomes]
rs12145858	0.85[EUR][1000 genomes]
rs6668608	0.90[EUR][1000 genomes]
rs74155466	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74155471	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74155478	0.81[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	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209535800-209550800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:209544400-209550200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:209546600-209552800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209546800-209550600	Enhancers	NHEK	skin
5	chr1:209547200-209549400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:209547400-209556000	Weak transcription	Esophagus	oesophagus
7	chr1:209548000-209550200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:209548400-209549600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:209548400-209549600	Enhancers	NHLF	lung
10	chr1:209548400-209550000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:209548400-209550000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:209548400-209550000	Enhancers	Hela-S3	cervix
13	chr1:209548400-209550000	Enhancers	Osteobl	bone
14	chr1:209548400-209550200	Enhancers	HMEC	breast
15	chr1:209548600-209549400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:209548600-209549400	Enhancers	Fetal Muscle Leg	muscle
17	chr1:209548600-209549600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:209548600-209549600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:209548600-209549600	Enhancers	Fetal Kidney	kidney
20	chr1:209548600-209549800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:209548600-209549800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:209548600-209549800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:209548600-209549800	Enhancers	HSMM	muscle
24	chr1:209548600-209550000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:209548600-209550200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:209548600-209550200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:209548600-209550200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:209548800-209549400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:209548800-209549400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:209548800-209549400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:209548800-209549600	Enhancers	NH-A	brain
32	chr1:209548800-209549800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:209548800-209550000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:209549000-209549400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:209549000-209549400	Weak transcription	Fetal Brain Male	brain
36	chr1:209549000-209549400	Enhancers	Fetal Lung	lung
37	chr1:209549000-209549400	Enhancers	NHDF-Ad	bronchial
38	chr1:209549000-209549800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:209549000-209549800	Enhancers	HSMMtube	muscle
40	chr1:209549000-209550600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:209549000-209552800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:209549200-209549400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr1:209549200-209549400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr1:209549200-209549400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr1:209549200-209549600	Enhancers	A549	lung
46	chr1:209549200-209549800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links