Variant report

Variant	rs1406917
Chromosome Location	chr1:120232281-120232282
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120167579..120169748-chr1:120230698..120233512,2	K562	blood:
2	chr1:120230713..120233125-chr1:120252907..120256114,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10218713	0.91[ASN][1000 genomes]
rs10494229	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10802132	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802133	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11577560	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs12057776	0.82[ASN][1000 genomes]
rs12127451	0.88[ASN][1000 genomes]
rs12562763	0.88[ASN][1000 genomes]
rs12565338	0.88[ASN][1000 genomes]
rs1441011	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1853048	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1886736	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2236398	0.88[JPT][hapmap]
rs4659226	0.91[ASN][1000 genomes]
rs55806106	0.88[ASN][1000 genomes]
rs60466603	0.90[ASN][1000 genomes]
rs6428840	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6683122	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs894079	0.84[JPT][hapmap]
rs942835	0.84[JPT][hapmap]

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:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120228400-120232400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:120228600-120233000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr1:120229000-120232400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:120230400-120232600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:120230400-120232800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:120231000-120233200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:120231200-120232400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:120231400-120232400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:120231400-120233000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:120231600-120232400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:120231600-120232600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:120231800-120233000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:120232000-120232600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:120232200-120232400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:120232200-120232400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:120232200-120232400	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links