Variant report

Variant	rs1810006
Chromosome Location	chr19:52838445-52838446
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52771196..52774040-chr19:52836837..52839956,3	MCF-7	breast:
2	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:
3	chr19:52641710..52644473-chr19:52838292..52841252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000204611	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10404965	0.94[ASN][1000 genomes]
rs10405321	0.94[ASN][1000 genomes]
rs10407594	0.91[ASN][1000 genomes]
rs10408636	0.91[ASN][1000 genomes]
rs10411053	0.94[ASN][1000 genomes]
rs10415728	0.91[ASN][1000 genomes]
rs10419765	0.89[ASN][1000 genomes]
rs11084148	0.94[ASN][1000 genomes]
rs12462904	0.90[ASN][1000 genomes]
rs12462953	0.90[ASN][1000 genomes]
rs1540745	0.94[ASN][1000 genomes]
rs167707	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs167708	0.88[ASN][1000 genomes]
rs170414	0.97[ASN][1000 genomes]
rs2115075	0.84[ASN][1000 genomes]
rs2115076	0.94[ASN][1000 genomes]
rs2657933	0.82[ASN][1000 genomes]
rs321902	0.87[ASN][1000 genomes]
rs321919	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs321921	0.96[ASN][1000 genomes]
rs321922	0.95[ASN][1000 genomes]
rs321923	0.96[ASN][1000 genomes]
rs321924	0.93[ASN][1000 genomes]
rs321925	0.95[ASN][1000 genomes]
rs321926	0.88[ASN][1000 genomes]
rs321928	0.85[ASN][1000 genomes]
rs321932	0.85[ASN][1000 genomes]
rs321934	0.84[ASN][1000 genomes]
rs321935	0.85[ASN][1000 genomes]
rs4801912	0.87[ASN][1000 genomes]
rs7247178	0.87[ASN][1000 genomes]
rs7249338	0.80[ASN][1000 genomes]
rs7249784	0.91[ASN][1000 genomes]
rs7256570	0.96[ASN][1000 genomes]
rs7258711	0.81[ASN][1000 genomes]
rs7260178	0.87[ASN][1000 genomes]
rs8102373	0.93[ASN][1000 genomes]
rs890842	0.84[ASN][1000 genomes]
rs890843	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
10	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1810006	ZNF480	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
2	chr19:52833000-52839400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:52836600-52838800	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:52836600-52838800	Weak transcription	Brain Substantia Nigra	brain
5	chr19:52836800-52838600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:52836800-52838600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr19:52836800-52838600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr19:52836800-52838800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:52836800-52839000	Weak transcription	Left Ventricle	heart
10	chr19:52837600-52838600	Weak transcription	Right Ventricle	heart
11	chr19:52838400-52838600	Enhancers	Dnd41	blood
12	chr19:52838400-52839000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:52838400-52839000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links