Variant report

Variant	rs660148
Chromosome Location	chr9:101127379-101127380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101125471..101128354-chr9:101130836..101133824,3	MCF-7	breast:
2	chr9:101125471..101127480-chr9:101134828..101138522,3	K562	blood:
3	chr9:101118065..101120527-chr9:101125284..101127411,2	K562	blood:
4	chr9:101116043..101117786-chr9:101124886..101127465,2	K562	blood:
5	chr9:101125220..101129376-chr9:101135603..101141784,6	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10818821	0.89[ASN][1000 genomes]
rs10818832	0.80[CHD][hapmap]
rs10818833	0.80[CHD][hapmap]
rs10986017	0.84[JPT][hapmap]
rs10986060	0.80[CHD][hapmap]
rs2572364	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3780428	0.80[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs3780429	0.80[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs3780430	0.80[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs3780432	0.85[JPT][hapmap]
rs473589	1.00[ASN][1000 genomes]
rs487422	0.88[ASN][1000 genomes]
rs487910	0.80[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.89[ASN][1000 genomes]
rs531529	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs545115	0.86[ASN][1000 genomes]
rs552989	0.85[JPT][hapmap]
rs567931	0.80[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs571569	0.81[GIH][hapmap]
rs583237	0.89[ASN][1000 genomes]
rs583641	0.90[GIH][hapmap];0.89[TSI][hapmap]
rs585325	0.80[CHB][hapmap]
rs585819	0.80[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs613308	0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs625500	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs628997	0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs648085	0.80[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs659768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[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]
rs661105	0.85[JPT][hapmap]
rs661532	0.85[JPT][hapmap]
rs669095	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs670807	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs693135	0.89[ASN][1000 genomes]
rs7023272	0.88[ASN][1000 genomes]
rs7039867	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs774334	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs774335	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs774344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs660148	NCBP1	cis	cerebellum	SCAN
rs660148	MRPL50	cis	cerebellum	SCAN
rs660148	HIATL1	cis	parietal	SCAN
rs660148	TEX10	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101118800-101127400	Weak transcription	Brain Germinal Matrix	brain
2	chr9:101118800-101127400	Weak transcription	Fetal Brain Female	brain
3	chr9:101120600-101134400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr9:101123200-101127400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:101126600-101142600	Weak transcription	Brain Angular Gyrus	brain
6	chr9:101126800-101128200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:101127000-101128800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:101127200-101127400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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