Variant report

Variant	rs10427858
Chromosome Location	chr22:29157875-29157876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29155529..29158980-chr22:29193770..29197123,3	MCF-7	breast:
2	chr22:29156118..29157971-chr22:29167441..29169542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000159873	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12330071	0.93[EUR][1000 genomes]
rs2206061	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2228260	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28448648	0.84[EUR][1000 genomes]
rs41281603	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56119508	1.00[EUR][1000 genomes]
rs5997389	0.84[AFR][1000 genomes]
rs5997390	0.84[AFR][1000 genomes]
rs5997401	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005856	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6005861	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005870	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005874	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005898	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005899	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60116790	0.92[AFR][1000 genomes]
rs73388803	0.84[AFR][1000 genomes]
rs9306460	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9620826	0.92[AFR][1000 genomes]
rs9620828	0.92[AFR][1000 genomes]
rs9620833	0.84[AFR][1000 genomes]
rs9625548	0.89[AFR][1000 genomes]
rs9625551	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9625554	0.81[AFR][1000 genomes]
rs9625558	0.84[EUR][1000 genomes]
rs9625565	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625568	0.92[AFR][1000 genomes]
rs9625572	0.92[AFR][1000 genomes]
rs9625575	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9625580	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv516312	chr22:29153759-29160314	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	6 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	chr22:29143600-29160000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:29145800-29168000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr22:29148000-29164400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:29148000-29167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:29149600-29165400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:29154400-29167400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr22:29156800-29160200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr22:29157000-29158200	Enhancers	Placenta	Placenta
9	chr22:29157000-29160800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr22:29157000-29161200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr22:29157600-29160000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr22:29157600-29160200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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