Variant report

Variant	rs10875718
Chromosome Location	chr12:48411102-48411103
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48395740..48398491-chr12:48410326..48412487,2	MCF-7	breast:
2	chr12:48409071..48411163-chr12:48439800..48441969,2	MCF-7	breast:
3	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

Variant related genes	Relation type
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10128967	1.00[CHB][hapmap]
rs10506276	1.00[CHB][hapmap]
rs10875716	0.84[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10875719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875721	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10875743	0.88[CEU][hapmap]
rs10875749	0.80[CEU][hapmap]
rs10875753	0.80[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs11168338	0.84[TSI][hapmap]
rs11168343	0.81[EUR][1000 genomes]
rs11168351	0.84[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11168408	0.88[CEU][hapmap]
rs11168428	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs11168437	0.88[GIH][hapmap];0.82[TSI][hapmap]
rs11574026	1.00[CHB][hapmap]
rs11830378	1.00[CHB][hapmap]
rs12228750	0.88[CEU][hapmap]
rs12297820	1.00[CHB][hapmap]
rs12301562	1.00[CHB][hapmap]
rs12368659	0.80[CEU][hapmap]
rs12816820	0.80[CEU][hapmap]
rs1476607	0.80[CEU][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs17224828	1.00[CHB][hapmap]
rs17225198	1.00[CHB][hapmap]
rs17823193	1.00[CHB][hapmap]
rs17823415	1.00[CHB][hapmap]
rs17823565	1.00[CHB][hapmap]
rs2051851	0.88[CEU][hapmap]
rs2408955	0.80[GIH][hapmap]
rs3997	0.88[CEU][hapmap]
rs4760612	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4760679	0.88[CEU][hapmap]
rs6580650	0.88[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6580652	0.88[EUR][1000 genomes]
rs7297558	1.00[CHB][hapmap]
rs7301003	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs7301509	1.00[CHB][hapmap]
rs7310935	1.00[CHB][hapmap]
rs7486941	0.83[GIH][hapmap]
rs7487682	0.83[GIH][hapmap]
rs7971880	0.84[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7975632	0.88[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes]
rs8716	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs973398	0.88[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10875718	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875718	LMBR1L	cis	cerebellum	SCAN
rs10875718	RAPGEF3	cis	parietal	SCAN
rs10875718	DDX23	cis	parietal	SCAN
rs10875718	OR6C70	trans	parietal	SCAN
rs10875718	H1FNT	cis	Muscle Skeletal	GTEx
rs10875718	PRPF40B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48407600-48411400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:48410200-48411400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48410200-48411600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48410200-48411600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:48410400-48411200	Enhancers	HMEC	breast
7	chr12:48410400-48411400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:48410400-48411600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48410600-48412400	Enhancers	Fetal Intestine Large	intestine
10	chr12:48410600-48414800	Weak transcription	Hela-S3	cervix
11	chr12:48410800-48412400	Enhancers	Fetal Intestine Small	intestine
12	chr12:48411000-48411200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:48411000-48411400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:48411000-48411400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr12:48411000-48411400	Flanking Active TSS	HepG2	liver

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