Variant report

Variant	rs11808966
Chromosome Location	chr1:77846143-77846144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77838249..77841580-chr1:77844120..77846924,3	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11162334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11162335	0.84[AFR][1000 genomes]
rs11809786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12078902	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61782700	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6672375	1.00[ASW][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11808966	MSH4	cis	cerebellum	SCAN
rs11808966	PIGK	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77835800-77846400	Weak transcription	Aorta	Aorta
2	chr1:77839000-77854000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:77842800-77846400	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:77843600-77846600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:77844800-77846600	Genic enhancers	NHDF-Ad	bronchial
6	chr1:77845000-77846200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:77845000-77852000	Weak transcription	Brain Anterior Caudate	brain
8	chr1:77845000-77853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:77845200-77846200	Weak transcription	NHLF	lung
10	chr1:77845200-77851200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:77845200-77851200	Weak transcription	Brain Substantia Nigra	brain
12	chr1:77845200-77853400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:77845200-77860000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
15	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:77845400-77852400	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:77845600-77847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:77845800-77846200	Strong transcription	HSMM	muscle
19	chr1:77845800-77846400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:77845800-77846400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:77845800-77846600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:77845800-77847600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:77845800-77848200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:77846000-77852000	Weak transcription	Brain Inferior Temporal Lobe	brain

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