Variant report

Variant	rs10875719
Chromosome Location	chr12:48411158-48411159
allele	C/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: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

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]
rs10875718	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	0.93[EUR][1000 genomes]
rs10875743	0.88[CEU][hapmap]
rs10875749	0.80[CEU][hapmap]
rs10875753	0.80[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs11168338	0.84[TSI][hapmap]
rs11168343	0.80[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];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs11168437	0.93[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];0.95[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	0.84[GIH][hapmap]
rs3997	0.88[CEU][hapmap]
rs4760612	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs4760679	0.88[CEU][hapmap]
rs6580650	0.88[CEU][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6580652	0.87[EUR][1000 genomes]
rs7297558	1.00[CHB][hapmap]
rs7301003	0.80[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs7301509	1.00[CHB][hapmap]
rs7310935	1.00[CHB][hapmap]
rs7315820	0.81[GIH][hapmap]
rs7486941	0.88[GIH][hapmap]
rs7487682	0.88[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];0.93[GIH][hapmap];0.84[MEX][hapmap];0.88[EUR][1000 genomes]
rs8716	0.80[CEU][hapmap];0.95[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10875719	H1FNT	cis	Muscle Skeletal	GTEx
rs10875719	PRPF40B	cis	parietal	SCAN
rs10875719	PFKM	cis	multi-tissue	Pritchard
rs10875719	OR6C70	trans	parietal	SCAN
rs10875719	LMBR1L	cis	cerebellum	SCAN
rs10875719	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875719	DDX23	cis	parietal	SCAN
rs10875719	RAPGEF3	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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