Variant report

Variant	rs575555
Chromosome Location	chr13:52437621-52437622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52376935..52378764-chr13:52436044..52437882,2	MCF-7	breast:
2	chr13:52433416..52435036-chr13:52436676..52439385,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102796	Chromatin interaction
ENSG00000231856	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12874582	1.00[ASN][1000 genomes]
rs1535577	1.00[CEU][hapmap]
rs17076052	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs1924614	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924615	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924618	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408530	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28429889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485335	1.00[ASN][1000 genomes]
rs34507703	1.00[ASN][1000 genomes]
rs34595679	1.00[ASN][1000 genomes]
rs35382547	1.00[ASN][1000 genomes]
rs35824984	1.00[ASN][1000 genomes]
rs4605048	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481797	1.00[CEU][hapmap]
rs549831	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577331	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs579839	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58050745	1.00[ASN][1000 genomes]
rs58919798	1.00[ASN][1000 genomes]
rs61957362	1.00[ASN][1000 genomes]
rs61957363	1.00[ASN][1000 genomes]
rs61957365	1.00[ASN][1000 genomes]
rs61957367	1.00[ASN][1000 genomes]
rs61957391	1.00[ASN][1000 genomes]
rs61957414	1.00[ASN][1000 genomes]
rs7323551	1.00[ASN][1000 genomes]
rs7324468	1.00[CEU][hapmap]
rs7333241	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7336182	1.00[ASN][1000 genomes]
rs7338168	1.00[ASN][1000 genomes]
rs932912	1.00[ASN][1000 genomes]
rs9596597	1.00[CEU][hapmap]
rs9596601	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs575555	LRTM1	trans	brain	seeQTL
rs575555	GUCA1C	trans	brain	seeQTL
rs575555	CRX	trans	brain	seeQTL
rs575555	GPR88	trans	brain	seeQTL
rs575555	SLC5A7	trans	brain	seeQTL
rs575555	SH2D2A	trans	brain	seeQTL
rs575555	TTR	trans	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52433800-52479400	Weak transcription	HepG2	liver
2	chr13:52436000-52438000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr13:52436600-52438000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:52436600-52438200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:52436600-52438200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:52437000-52438000	Enhancers	Fetal Thymus	thymus
7	chr13:52437600-52438200	Enhancers	Right Atrium	heart

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