Variant report

Variant	rs10919239
Chromosome Location	chr1:169752700-169752701
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169751349..169757764-chr1:169760418..169766538,11	K562	blood:
2	chr1:169453908..169455963-chr1:169751227..169752986,2	K562	blood:
3	chr1:169751559..169753241-chr1:169780241..169782649,2	MCF-7	breast:
4	chr1:169750643..169754945-chr1:169761592..169765030,6	MCF-7	breast:
5	chr1:169751762..169754671-chr1:169756355..169758348,3	K562	blood:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10733054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737549	0.91[CEU][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs10753792	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753793	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800479	0.84[EUR][1000 genomes]
rs10800480	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs10800481	0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs10800483	0.95[CEU][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs10800484	0.80[JPT][hapmap]
rs10800485	0.95[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs10800486	0.91[CEU][hapmap]
rs10919230	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10919245	0.84[EUR][1000 genomes]
rs10919248	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs10919251	0.84[EUR][1000 genomes]
rs12133843	0.91[CEU][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.80[EUR][1000 genomes]
rs1534904	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1883436	0.80[EUR][1000 genomes]
rs2056980	0.87[CEU][hapmap]
rs2056981	0.91[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2179396	0.95[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs2205848	0.91[CHD][hapmap];0.94[MEX][hapmap]
rs2205850	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2205851	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281039	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2294322	0.84[EUR][1000 genomes]
rs2294496	0.80[JPT][hapmap]
rs2420512	0.84[EUR][1000 genomes]
rs2420514	0.95[CEU][hapmap]
rs2750016	0.84[CEU][hapmap]
rs2806386	0.87[CEU][hapmap]
rs2806393	0.83[CEU][hapmap]
rs3753308	0.95[CEU][hapmap]
rs3766132	0.95[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3766134	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3766137	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs3766142	0.81[EUR][1000 genomes]
rs3766148	0.91[CEU][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs3766151	0.88[ASW][hapmap];0.91[CEU][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap]
rs3766154	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs3917390	0.83[EUR][1000 genomes]
rs3917412	0.82[CHD][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs3917434	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4508080	0.95[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs4614317	0.95[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs4615900	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs4656196	0.91[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656197	0.80[JPT][hapmap]
rs4656716	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656721	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4656724	0.80[JPT][hapmap]
rs6427217	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427220	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs6427224	0.80[JPT][hapmap]
rs6427225	0.95[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6427227	0.80[JPT][hapmap]
rs6656965	0.83[EUR][1000 genomes]
rs6664099	0.80[JPT][hapmap]
rs6670818	0.95[CEU][hapmap];0.80[TSI][hapmap]
rs6676810	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680650	0.84[EUR][1000 genomes]
rs6682835	0.95[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs6683056	0.95[CEU][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6687377	0.80[JPT][hapmap]
rs717481	0.83[EUR][1000 genomes]
rs732185	0.91[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs7515714	0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518441	0.83[ASN][1000 genomes]
rs7525259	0.91[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs7526261	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530237	0.91[CEU][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7538317	0.83[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7545011	0.84[EUR][1000 genomes]
rs9287097	0.91[CEU][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs964827	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10919239	C1orf112	cis	cerebellum	SCAN
rs10919239	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs10919239	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169748200-169753600	Enhancers	HUVEC	blood vessel
2	chr1:169749400-169761400	Weak transcription	Liver	Liver
3	chr1:169750200-169753000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:169750400-169754400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:169750800-169762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:169751600-169753000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:169751600-169760200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:169751600-169762600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:169752000-169753200	Weak transcription	HMEC	breast
10	chr1:169752600-169760200	Weak transcription	Placenta Amnion	Placenta Amnion

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