Variant report

Variant	rs1889556
Chromosome Location	chr6:114479520-114479521
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1022387	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153467	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13199095	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1401771	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1964777	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1964778	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945991	0.94[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs884817	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9320480	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9374439	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9387192	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9481423	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9481425	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9481432	0.88[YRI][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	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv1034897	chr6:114454186-114555679	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv34434	chr6:114465305-115462799	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1029370	chr6:114471446-114566884	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1889556	FAM26D	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114468800-114479800	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:114472000-114479800	Weak transcription	Brain Angular Gyrus	brain
3	chr6:114472800-114480000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:114476200-114489400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:114476200-114493600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:114476200-114497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:114476400-114488200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:114476400-114488800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:114476800-114489400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:114477000-114491800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:114478400-114481000	Enhancers	Fetal Intestine Small	intestine
12	chr6:114478400-114488200	Weak transcription	Brain Anterior Caudate	brain
13	chr6:114478600-114480400	Weak transcription	Brain Substantia Nigra	brain
14	chr6:114479000-114479600	Enhancers	Duodenum Mucosa	Duodenum
15	chr6:114479000-114480600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr6:114479200-114481200	Weak transcription	Stomach Mucosa	stomach
17	chr6:114479200-114482600	Enhancers	HepG2	liver
18	chr6:114479400-114483600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:114479400-114489400	Weak transcription	Pancreas	Pancrea

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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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