Variant report

Variant	rs6989059
Chromosome Location	chr8:130118208-130118209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10107597	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12546355	0.87[AMR][1000 genomes]
rs12547572	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13263573	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459683	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540589	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28628837	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448233	0.82[AMR][1000 genomes]
rs4524751	0.82[AMR][1000 genomes]
rs4524752	0.82[AMR][1000 genomes]
rs6470695	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470697	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6989504	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996102	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7004434	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7824972	0.82[EUR][1000 genomes]
rs7825362	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7846150	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][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	nsv891442	chr8:130016499-130130604	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv891443	chr8:130016499-130220746	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv891444	chr8:130024642-130130604	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv612228	chr8:130115644-130130604	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6989059	NEU2	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:130115000-130119200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr8:130115200-130119000	Enhancers	NHEK	skin
3	chr8:130115200-130119200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:130115400-130118600	Enhancers	HMEC	breast
5	chr8:130115400-130118800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr8:130115400-130119000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr8:130115600-130126800	Genic enhancers	Dnd41	blood
8	chr8:130116200-130124400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr8:130116400-130119400	Weak transcription	Thymus	Thymus
10	chr8:130116400-130126000	Weak transcription	Pancreas	Pancrea
11	chr8:130116400-130127200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:130118000-130118400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:130118000-130118600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:130118000-130118800	ZNF genes & repeats	Fetal Thymus	thymus
15	chr8:130118200-130124000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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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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