Variant report

Variant	rs2444779
Chromosome Location	chr5:43203125-43203126
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	chr5:43192678..43195533-chr5:43199864..43203293,3	K562	blood:

Variant related genes	Relation type
ENSG00000177453	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12108783	0.84[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes]
rs12655504	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1574407	0.88[YRI][hapmap]
rs160709	0.88[YRI][hapmap]
rs1618891	0.87[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap]
rs1624415	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[YRI][hapmap]
rs1670796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs222060	0.88[YRI][hapmap]
rs2330089	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs309914	0.88[YRI][hapmap]
rs316404	0.88[YRI][hapmap]
rs316408	0.88[YRI][hapmap]
rs316413	0.84[YRI][hapmap]
rs316414	0.88[YRI][hapmap]
rs36116359	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4428420	0.88[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes]
rs4866811	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs512921	0.83[CEU][hapmap];0.80[CHB][hapmap];0.80[YRI][hapmap]
rs557076	0.81[CHB][hapmap]
rs567884	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap]
rs57412930	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59733223	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62368886	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs643307	0.88[YRI][hapmap]
rs6892422	0.86[ASW][hapmap];0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap]
rs7734884	0.84[AMR][1000 genomes]
rs782971	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs782978	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap]
rs782984	0.81[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap]
rs903391	0.88[CEU][hapmap];0.80[CHB][hapmap];0.87[YRI][hapmap]
rs9292862	0.88[YRI][hapmap]
rs9292867	0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2444779	ZNF131	Cis_1M	lymphoblastoid	RTeQTL
rs2444779	TTLL7	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43195000-43203200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:43195000-43209000	Weak transcription	Brain Substantia Nigra	brain
3	chr5:43196200-43208800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:43196200-43245400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:43196400-43205000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:43196400-43208800	Weak transcription	Brain Angular Gyrus	brain
7	chr5:43196400-43208800	Weak transcription	Brain Hippocampus Middle	brain
8	chr5:43196400-43208800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:43196400-43209200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:43198600-43208800	Weak transcription	Brain Anterior Caudate	brain
11	chr5:43200600-43203200	Enhancers	GM12878-XiMat	blood
12	chr5:43202200-43203600	Enhancers	K562	blood
13	chr5:43202400-43203200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:43202600-43203600	Enhancers	Stomach Mucosa	stomach
15	chr5:43202800-43204000	Enhancers	Osteobl	bone

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