Variant report

Variant	rs274293
Chromosome Location	chr10:25265047-25265048
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:25258984..25265341-chr10:25266551..25271124,6	MCF-7	breast:
2	chr10:25245687..25248875-chr10:25261943..25265245,3	MCF-7	breast:
3	chr10:25244301..25246252-chr10:25263526..25265858,2	K562	blood:
4	chr10:25263858..25265839-chr10:25269718..25271619,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1000875	0.82[CHB][hapmap]
rs10508685	0.82[CHB][hapmap]
rs10508686	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap]
rs10764515	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10764518	0.82[CHB][hapmap]
rs10764519	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap]
rs10828741	0.82[CHB][hapmap]
rs10828745	0.82[CHB][hapmap]
rs10828751	0.85[CEU][hapmap]
rs11014357	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap]
rs12249889	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap]
rs12256642	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs12761282	0.82[ASN][1000 genomes]
rs12784769	0.81[CEU][hapmap];0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs1492608	0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap]
rs1546097	0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs166670	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16925207	0.93[ASN][1000 genomes]
rs185669	0.80[CEU][hapmap]
rs2031600	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2131276	0.82[CHB][hapmap]
rs2279547	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291583	0.91[CHD][hapmap];0.84[GIH][hapmap]
rs2307047	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs274288	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274289	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274290	0.81[ASN][1000 genomes]
rs274291	0.92[ASN][1000 genomes]
rs274292	0.92[ASN][1000 genomes]
rs274294	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274301	0.92[CEU][hapmap];0.87[CHB][hapmap];0.80[EUR][1000 genomes]
rs274304	0.81[CEU][hapmap]
rs274305	0.84[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs274311	0.84[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap]
rs274313	0.84[CEU][hapmap]
rs274316	0.84[CEU][hapmap]
rs2818289	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4345864	0.82[CHB][hapmap]
rs4556443	0.85[EUR][1000 genomes]
rs4748993	0.80[CEU][hapmap]
rs4748996	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs4749000	0.80[GIH][hapmap]
rs6482467	0.82[CHB][hapmap]
rs6482468	0.88[CEU][hapmap]
rs7086282	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap]
rs7393543	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap]
rs7913853	0.82[CHB][hapmap]
rs902903	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs902904	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs902905	0.82[CHB][hapmap]
rs987274	0.81[CEU][hapmap];0.82[CHB][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	nsv1053278	chr10:25140776-25269093	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs274293	THNSL1	cis	cerebellum	SCAN
rs274293	PIP4K2A	cis	parietal	SCAN
rs274293	ANKRD9	trans	cerebellum	SCAN
rs274293	THNSL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25259200-25269000	Weak transcription	Brain Anterior Caudate	brain
2	chr10:25262400-25269200	Weak transcription	Brain Hippocampus Middle	brain
3	chr10:25263400-25265400	Enhancers	Fetal Lung	lung
4	chr10:25263400-25272000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr10:25263600-25265200	Enhancers	NHLF	lung
6	chr10:25264000-25265200	Enhancers	Fetal Muscle Leg	muscle
7	chr10:25264400-25267200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:25264400-25271600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:25264400-25277600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:25264400-25277800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:25264400-25281800	Weak transcription	Fetal Intestine Small	intestine
12	chr10:25264600-25266400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:25264600-25292200	Weak transcription	Ovary	ovary
14	chr10:25264800-25268200	Weak transcription	Brain Substantia Nigra	brain
15	chr10:25265000-25272800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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