Variant report

Variant	rs6667906
Chromosome Location	chr1:209560500-209560501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209538239..209540335-chr1:209559472..209561618,2	MCF-7	breast:
2	chr1:209555303..209558478-chr1:209558595..209562675,4	MCF-7	breast:
3	chr1:209554903..209565803-chr1:209600283..209609508,22	MCF-7	breast:
4	chr1:209560392..209562273-chr1:209582844..209585455,2	MCF-7	breast:
5	chr1:209556562..209561769-chr1:209603992..209608152,7	MCF-7	breast:
6	chr1:209537992..209540217-chr1:209560334..209562277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230937	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11811038	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135550	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140933	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12142844	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12142846	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12144725	0.86[AFR][1000 genomes]
rs1354851	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1857967	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986792	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55717527	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60460414	0.82[AFR][1000 genomes]
rs6674793	0.90[AFR][1000 genomes]
rs74155478	0.84[AFR][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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209550200-209560600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:209553200-209568600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:209555200-209561000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:209555400-209560800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:209555400-209561000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:209555600-209564400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:209555800-209565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:209556600-209560800	Weak transcription	Esophagus	oesophagus
9	chr1:209556800-209560800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:209557000-209560600	Weak transcription	Placenta	Placenta
11	chr1:209557000-209560800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:209557000-209560800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:209557200-209561600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:209557400-209560800	Weak transcription	Osteobl	bone
15	chr1:209557800-209561200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:209557800-209565200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:209558000-209562000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:209558000-209566200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:209558200-209560600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:209558200-209564400	Enhancers	HMEC	breast
21	chr1:209558400-209560600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:209558400-209564400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:209559000-209560800	Weak transcription	HSMMtube	muscle
24	chr1:209559200-209560600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:209559400-209561200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:209559400-209565200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:209559400-209566000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:209559600-209560600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:209560000-209563000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:209560200-209561600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:209560400-209560800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:209560400-209561000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:209560400-209561600	Flanking Active TSS	NHEK	skin
34	chr1:209560400-209563600	Enhancers	HSMM	muscle

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