Variant report

Variant	rs4146299
Chromosome Location	chr3:119999820-119999821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119998538..120000450-chr3:120002439..120005114,2	K562	blood:
2	chr3:119993238..119995408-chr3:119999571..120001166,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175697	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1056928	1.00[JPT][hapmap]
rs1147696	1.00[JPT][hapmap]
rs1147698	1.00[JPT][hapmap]
rs1147699	1.00[JPT][hapmap]
rs12494395	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1259328	1.00[JPT][hapmap]
rs13061630	1.00[JPT][hapmap]
rs13073885	1.00[JPT][hapmap]
rs13081675	1.00[JPT][hapmap]
rs13081694	1.00[JPT][hapmap]
rs13091848	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13096256	1.00[JPT][hapmap]
rs13097755	1.00[JPT][hapmap]
rs13100865	1.00[JPT][hapmap]
rs13709	1.00[JPT][hapmap]
rs1492272	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1515577	1.00[JPT][hapmap]
rs17813772	1.00[JPT][hapmap]
rs1969356	1.00[JPT][hapmap]
rs2029607	1.00[JPT][hapmap]
rs2030414	1.00[JPT][hapmap]
rs2091726	1.00[JPT][hapmap]
rs2272515	1.00[JPT][hapmap]
rs2319670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488	1.00[JPT][hapmap]
rs34014378	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34829073	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34964758	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34998142	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35587339	0.83[EUR][1000 genomes]
rs35964791	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4146300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs4378995	0.81[EUR][1000 genomes]
rs4676676	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4676698	1.00[JPT][hapmap]
rs4676703	1.00[JPT][hapmap]
rs4676776	1.00[JPT][hapmap]
rs4676778	1.00[JPT][hapmap]
rs4676779	1.00[JPT][hapmap]
rs4676781	1.00[JPT][hapmap]
rs4676782	1.00[JPT][hapmap]
rs4676783	1.00[JPT][hapmap]
rs4676811	1.00[JPT][hapmap]
rs55861253	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56103727	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6438574	0.81[AMR][1000 genomes]
rs6438575	1.00[JPT][hapmap]
rs66815350	0.84[EUR][1000 genomes]
rs6771116	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774960	0.82[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6776878	1.00[JPT][hapmap]
rs6792814	1.00[JPT][hapmap]
rs6795868	0.80[EUR][1000 genomes]
rs6803846	0.80[EUR][1000 genomes]
rs7612000	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs869247	1.00[JPT][hapmap]
rs9843220	0.85[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9875613	0.81[EUR][1000 genomes]
rs9880550	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv2763294	chr3:119994092-120003434	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4146299	RABL3	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links