Variant report

Variant	rs1980449
Chromosome Location	chr6:25629658-25629659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1012899	0.88[GIH][hapmap]
rs1074706	0.80[YRI][hapmap]
rs1980448	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010291	0.80[YRI][hapmap]
rs2011472	0.80[YRI][hapmap]
rs2281073	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6900762	0.81[ASW][hapmap];0.80[YRI][hapmap]
rs6932536	0.80[YRI][hapmap]
rs932319	0.80[YRI][hapmap]
rs9393654	0.80[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1980449	HIST1H2BI	cis	cerebellum	SCAN
rs1980449	HIST1H3G	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25613200-25631000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:25622800-25634800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:25625200-25630600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:25627400-25631800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:25628000-25630000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:25628200-25631800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:25628600-25629800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:25628600-25632000	Enhancers	HepG2	liver
9	chr6:25629000-25638200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:25629200-25629800	Enhancers	Liver	Liver
11	chr6:25629200-25629800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:25629400-25630200	Enhancers	Pancreas	Pancrea
13	chr6:25629600-25629800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr6:25629600-25629800	Enhancers	HUES6 Cell Line	embryonic stem cell

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

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