Variant report

Variant	rs12072780
Chromosome Location	chr1:120228195-120228196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158797	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs10158823	1.00[MEX][hapmap]
rs10802131	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs10923886	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs10923922	1.00[MEX][hapmap]
rs12030925	0.93[ASW][hapmap];0.91[YRI][hapmap]
rs12057495	1.00[MEX][hapmap]
rs12082229	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs12086499	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17024340	1.00[MEX][hapmap]
rs6662742	1.00[EUR][1000 genomes]
rs7555981	1.00[EUR][1000 genomes]

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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120222600-120228400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:120222600-120229000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:120222600-120229000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:120222800-120228200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:120222800-120228600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:120222800-120229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:120222800-120229000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:120222800-120231400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:120223200-120229000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:120225800-120229400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:120227000-120231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:120227200-120228400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:120227200-120228400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:120227200-120228600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:120227200-120228600	Weak transcription	NHEK	skin
16	chr1:120227200-120228800	Weak transcription	HMEC	breast
17	chr1:120227200-120229000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:120227200-120229000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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