Variant report

Variant	rs56266442
Chromosome Location	chr2:186483964-186483965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10174315	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180772	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10186909	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10189129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190576	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10209067	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10490389	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1075257	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682752	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684181	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11686533	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694100	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11891430	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891748	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904219	0.94[ASN][1000 genomes]
rs12328928	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12328996	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13410805	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13412749	0.88[EUR][1000 genomes]
rs13421326	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13421575	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17813140	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17815052	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28508191	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35119381	0.95[EUR][1000 genomes]
rs35379699	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35939893	0.94[ASN][1000 genomes]
rs59153366	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59486260	0.81[EUR][1000 genomes]
rs6713671	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716541	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749407	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6752510	0.94[ASN][1000 genomes]
rs6753178	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6755533	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761099	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72894199	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72896010	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72896445	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72896480	0.90[EUR][1000 genomes]
rs7593451	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7606908	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs918229	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004048	chr2:186303297-186541503	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875531	chr2:186303530-186489537	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv875536	chr2:186309738-186504175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv875540	chr2:186345148-186583961	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv875541	chr2:186345148-186598526	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1006219	chr2:186352780-186524793	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv584017	chr2:186352959-186515328	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv584018	chr2:186352959-186598526	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv916442	chr2:186356363-186534152	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv875543	chr2:186365918-186489537	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1000814	chr2:186391490-186520872	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1007052	chr2:186441382-186864390	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv584019	chr2:186445393-186866874	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1000561	chr2:186450293-186556017	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1009118	chr2:186450293-186864390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1004422	chr2:186463915-186556017	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv2763034	chr2:186473461-186587890	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1008230	chr2:186474069-186818718	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv536076	chr2:186474069-186818718	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv584020	chr2:186475590-186661567	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv584021	chr2:186475590-186866841	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	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
rs56266442	PART1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186483400-186484000	Enhancers	HMEC	breast
2	chr2:186483600-186484000	Enhancers	NHEK	skin
3	chr2:186483800-186490400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links