Variant report

Variant	rs2140765
Chromosome Location	chr3:143213741-143213742
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143212932..143214521-chr3:143217945..143220851,2	MCF-7	breast:
2	chr3:143205251..143209634-chr3:143211909..143216344,4	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13325345	0.80[AMR][1000 genomes]
rs1525007	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525009	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723033	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17640527	1.00[MKK][hapmap]
rs2049503	1.00[MKK][hapmap]
rs28518169	0.80[AMR][1000 genomes]
rs28679565	0.80[AMR][1000 genomes]
rs66623546	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708484	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73144723	1.00[ASN][1000 genomes]
rs838599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838602	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs838613	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838616	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838618	0.94[CEU][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838620	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838623	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838627	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838630	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838634	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838635	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838636	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838637	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838643	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838644	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838646	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838648	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838649	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs865710	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289661	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819535	0.80[AMR][1000 genomes]
rs9844522	1.00[MKK][hapmap]
rs9849487	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2140765	CRCT1	trans	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143174400-143220400	Weak transcription	Fetal Lung	lung
2	chr3:143176800-143220400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:143179400-143220400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:143185800-143213800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:143186000-143215600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:143186000-143223000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:143191400-143231000	Weak transcription	Primary B cells from cord blood	blood
8	chr3:143192400-143215200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:143200200-143213800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:143201800-143226400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:143209000-143214000	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:143209000-143226800	Weak transcription	Adipose Nuclei	Adipose
13	chr3:143211600-143214200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:143212000-143214800	Weak transcription	Placenta	Placenta
15	chr3:143212600-143224800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:143212600-143247400	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links