Variant report

Variant	rs45480993
Chromosome Location	chr1:46858669-46858670
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	POLR2A	chr1:46858482-46859533	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:46858498-46859042	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr1:46858535-46859392	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr1:46858370-46860721	H1-hESC	embryonic stem cell:	n/a	n/a
5	SETDB1	chr1:46858644-46860059	K562	blood:	n/a	chr1:46859968-46859977

Variant related genes	Relation type
FAAH	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10252	0.83[ASN][1000 genomes]
rs11211271	0.86[ASN][1000 genomes]
rs11804189	0.84[ASN][1000 genomes]
rs12073998	0.84[ASN][1000 genomes]
rs12075550	0.83[ASN][1000 genomes]
rs12563610	0.85[ASN][1000 genomes]
rs324416	0.91[ASN][1000 genomes]
rs3863641	0.84[ASN][1000 genomes]
rs3891758	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4110477	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41293281	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs41294484	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45540335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45564237	0.91[ASN][1000 genomes]
rs45577432	0.88[ASN][1000 genomes]
rs4660345	0.85[ASN][1000 genomes]
rs4660925	0.87[ASN][1000 genomes]
rs56733721	0.84[ASN][1000 genomes]
rs58710660	0.93[ASN][1000 genomes]
rs59082884	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60519942	0.93[ASN][1000 genomes]
rs61221162	0.91[ASN][1000 genomes]
rs61784604	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs873978	0.87[ASN][1000 genomes]
rs913168	0.90[ASN][1000 genomes]
rs9865	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46829400-46859400	Weak transcription	Brain Substantia Nigra	brain
2	chr1:46834600-46859600	Weak transcription	Psoas Muscle	Psoas
3	chr1:46836200-46859400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:46851000-46859800	Weak transcription	Ovary	ovary
5	chr1:46858000-46859400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:46858200-46859600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:46858200-46860000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:46858400-46859000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
9	chr1:46858400-46859200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
10	chr1:46858400-46859600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:46858400-46859600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:46858400-46859800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:46858400-46860800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr1:46858600-46858800	Active TSS	Primary T cells from cord blood	blood
15	chr1:46858600-46859000	ZNF genes & repeats	Right Atrium	heart
16	chr1:46858600-46859600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:46858600-46859800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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