Variant report

Variant	rs2248055
Chromosome Location	chr8:125966828-125966829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:125965221..125967859-chr8:126009015..126011042,3	MCF-7	breast:
2	chr8:125935909..125938271-chr8:125963994..125966987,3	MCF-7	breast:
3	chr8:125966414..125968159-chr8:125969946..125971937,2	MCF-7	breast:
4	chr8:125964835..125966928-chr8:125968756..125971401,2	K562	blood:
5	chr8:125826052..125829315-chr8:125964777..125971300,8	K562	blood:
6	chr8:125962308..125964397-chr8:125966591..125968437,2	K562	blood:
7	chr8:125964812..125967573-chr8:125978469..125981385,2	MCF-7	breast:
8	chr8:125921782..125924509-chr8:125964835..125967359,2	K562	blood:
9	chr8:125604776..125605783-chr8:125965786..125967049,3	MCF-7	breast:
10	chr8:125853620..125856478-chr8:125964634..125966898,2	K562	blood:
11	chr8:125962237..125964397-chr8:125966163..125968875,2	MCF-7	breast:
12	chr8:125550000..125552039-chr8:125965620..125968029,2	MCF-7	breast:
13	chr8:125593451..125595490-chr8:125966290..125968595,2	K562	blood:
14	chr8:125826052..125832853-chr8:125963334..125969415,10	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000104549	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000253513	Chromatin interaction
ENSG00000255491	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10099730	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1427087	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1427093	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2555726	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2555727	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[YRI][hapmap]
rs2590668	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2590669	0.82[CHB][hapmap]
rs2590670	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590672	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2590674	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2725879	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs2725881	0.83[CHB][hapmap];0.81[CHD][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	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030803	chr8:125868684-125969635	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1024405	chr8:125868684-125971035	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1020502	chr8:125868684-125972572	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2248055	HAS2	cis	cerebellum	SCAN
rs2248055	ZHX2	cis	cerebellum	SCAN
rs2248055	KLHL38	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125960000-125969400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:125966200-125967000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:125966400-125967200	Flanking Active TSS	K562	blood
4	chr8:125966400-125968400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:125966400-125969600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr8:125966600-125968200	Weak transcription	Fetal Thymus	thymus
7	chr8:125966800-125967000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr8:125966800-125967000	Enhancers	Fetal Heart	heart
9	chr8:125966800-125968000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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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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