Variant report

Variant	rs12139847
Chromosome Location	chr1:209554269-209554270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209553994..209556272-chr1:209567588..209570552,2	MCF-7	breast:
2	chr1:209551724..209554636-chr1:209607161..209609354,2	MCF-7	breast:
3	chr1:209544387..209547089-chr1:209552182..209554655,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231648	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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12119464	1.00[AMR][1000 genomes];0.94[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];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12120796	0.81[EUR][1000 genomes]
rs12121931	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12124710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12125358	0.90[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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12135244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.90[EUR][1000 genomes]
rs12140172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144443	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12144663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12144725	0.88[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	0.88[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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209547400-209556000	Weak transcription	Esophagus	oesophagus
2	chr1:209549400-209556200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:209549400-209556600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:209549600-209557200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:209549800-209560400	Weak transcription	HSMM	muscle
6	chr1:209550000-209555400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:209550000-209555400	Weak transcription	Fetal Brain Male	brain
8	chr1:209550200-209555200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:209550200-209555400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:209550200-209555400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:209550200-209560600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:209551000-209554800	Enhancers	NHEK	skin
13	chr1:209551800-209556400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:209552800-209555600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:209553200-209555800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:209553200-209556000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:209553200-209568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:209553400-209555400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:209553400-209556000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:209553400-209556000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:209553400-209556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:209553400-209556600	Weak transcription	Osteobl	bone
23	chr1:209553600-209556000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:209554000-209555400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:209554200-209555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:209554200-209555400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:209554200-209555600	Weak transcription	HMEC	breast
28	chr1:209554200-209556400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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