Variant report

Variant	rs10424369
Chromosome Location	chr19:19345356-19345357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr19:19345036-19345415	K562	blood:	n/a	n/a
2	CBX3	chr19:19345040-19345452	HCT-116	colon:	n/a	n/a
3	CBX3	chr19:19344929-19345439	K562	blood:	n/a	n/a
4	KAP1	chr19:19344892-19345470	K562	blood:	n/a	n/a
5	SETDB1	chr19:19344947-19345501	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19341601..19343468-chr19:19345129..19347319,3	K562	blood:

Variant related genes	Relation type
NCAN	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10403859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406659	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10411761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418279	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11667950	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11668677	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11668734	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11671506	1.00[CEU][hapmap]
rs11671527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13345554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17683766	1.00[CEU][hapmap]
rs17751021	1.00[CEU][hapmap]
rs2228600	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238672	0.88[YRI][hapmap]
rs2238674	0.96[EUR][1000 genomes]
rs2283627	0.88[EUR][1000 genomes]
rs28393849	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28409009	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28446016	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28508263	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28510494	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28541794	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28628330	0.87[AMR][1000 genomes]
rs28838696	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34673002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35583425	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761080	0.88[EUR][1000 genomes]
rs73922843	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19344000-19346000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:19344000-19347200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:19344200-19345800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
4	chr19:19344200-19346000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:19344200-19346000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
6	chr19:19344200-19346000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
7	chr19:19344200-19347400	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr19:19344400-19346000	ZNF genes & repeats	Fetal Brain Female	brain
9	chr19:19344600-19345800	ZNF genes & repeats	Brain Angular Gyrus	brain
10	chr19:19344600-19345800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
11	chr19:19344600-19346000	ZNF genes & repeats	Brain Anterior Caudate	brain
12	chr19:19344600-19346000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:19344800-19345400	Weak transcription	Fetal Brain Male	brain
14	chr19:19344800-19345800	ZNF genes & repeats	Brain Hippocampus Middle	brain
15	chr19:19345000-19346000	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr19:19345200-19346000	ZNF genes & repeats	Brain Substantia Nigra	brain

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