Variant report

Variant	rs602848
Chromosome Location	chr6:131446791-131446792
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10499180	1.00[CHB][hapmap]
rs11968011	1.00[CHB][hapmap]
rs1406456	1.00[CHB][hapmap]
rs1528863	1.00[CHB][hapmap]
rs17060018	1.00[CHB][hapmap]
rs1977577	1.00[CHB][hapmap]
rs473556	1.00[ASN][1000 genomes]
rs600306	0.92[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7766938	1.00[CHB][hapmap]
rs871628	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019112	chr6:131409284-131452300	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2761029	chr6:131413789-131452312	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1016925	chr6:131418532-131452300	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Migraine with aura	23793025	GWAS catalog
Migraine - clinic-based	23793025	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs602848	HBS1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131443600-131451000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:131445200-131447200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:131445200-131447200	Enhancers	NHEK	skin
4	chr6:131445400-131447200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:131445400-131447200	Enhancers	HMEC	breast
6	chr6:131446000-131451000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:131446000-131456200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:131446400-131446800	Enhancers	A549	lung
9	chr6:131446400-131447200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr6:131446400-131447200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:131446600-131446800	Enhancers	HSMMtube	muscle
12	chr6:131446600-131447000	Enhancers	HSMM	muscle
13	chr6:131446600-131447000	Enhancers	NH-A	brain
14	chr6:131446600-131447000	Enhancers	NHDF-Ad	bronchial
15	chr6:131446600-131447000	Enhancers	NHLF	lung

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links