Variant report

Variant	rs2872960
Chromosome Location	chr2:133271993-133271994
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1075655	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11687198	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11694982	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12691821	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13001535	0.91[CEU][hapmap];0.88[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13019326	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13030799	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13389584	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13401957	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13414365	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35405726	0.82[EUR][1000 genomes]
rs4284884	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4481050	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4485608	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4637177	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4954331	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4954334	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56747201	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558583	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7577419	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7595520	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs764716	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9646690	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999341	chr2:132714332-133358577	Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
2	nsv916487	chr2:132719325-133355859	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
3	nsv1009861	chr2:132719550-133358577	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
4	esv2763165	chr2:132719550-133358589	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
5	nsv431701	chr2:132722012-133356398	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
6	nsv526029	chr2:132733281-133351415	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
7	nsv999965	chr2:132743229-133358577	Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
8	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers 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
9	nsv459418	chr2:133034154-133348083	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv583149	chr2:133034154-133348083	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv583150	chr2:133034154-133351703	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv1004841	chr2:133124355-133350008	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv583153	chr2:133167263-133361282	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
15	nsv834378	chr2:133169796-133349406	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1014306	chr2:133252736-133402581	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv535925	chr2:133252736-133402581	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv583155	chr2:133253386-133415170	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	esv2756947	chr2:133267847-133313845	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv2759093	chr2:133267847-133313845	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2872960	LOC440905	cis	cerebellum	SCAN
rs2872960	R3HDM1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133262000-133280400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:133266000-133275000	Weak transcription	A549	lung
3	chr2:133268200-133282800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:133269400-133278400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:133271600-133272600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:133271800-133274400	Enhancers	Pancreas	Pancrea

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