Variant report

Variant	rs828858
Chromosome Location	chr2:74422194-74422195
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
2	chr2:74421259..74423609-chr2:74425242..74427996,3	MCF-7	breast:
3	chr2:74367938..74377304-chr2:74421816..74428438,25	K562	blood:
4	chr2:74404780..74407960-chr2:74421791..74423519,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114978	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1095968	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13426653	0.82[EUR][1000 genomes]
rs1667601	0.88[CEU][hapmap]
rs1723281	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1723285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853016	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546893	0.86[EUR][1000 genomes]
rs6546894	0.81[EUR][1000 genomes]
rs702462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7340453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587117	1.00[CHB][hapmap]
rs8001	0.81[EUR][1000 genomes]
rs828853	0.82[EUR][1000 genomes]
rs828855	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828856	0.86[EUR][1000 genomes]
rs828857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828859	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828882	0.81[CEU][hapmap]
rs828883	0.81[CEU][hapmap]
rs828884	0.81[CEU][hapmap]
rs828888	0.81[CEU][hapmap]
rs828903	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs844168	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74415600-74425200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:74415600-74425200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:74417200-74425000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:74417600-74425200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:74419400-74424400	Weak transcription	Pancreas	Pancrea
6	chr2:74419600-74425200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:74419800-74423800	Weak transcription	K562	blood
8	chr2:74419800-74425000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:74419800-74425200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:74420000-74425200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:74420400-74424800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:74421800-74423200	Enhancers	HepG2	liver

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