Variant report

Variant	rs4461258
Chromosome Location	chr2:152429679-152429680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10167358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.80[LWK][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10172023	0.83[ASN][1000 genomes]
rs10173699	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs10174077	0.83[ASN][1000 genomes]
rs10186656	0.82[ASN][1000 genomes]
rs1047957	0.86[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs10497081	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10497082	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1061305	0.89[CHD][hapmap];0.88[JPT][hapmap]
rs11892439	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12618981	0.82[CEU][hapmap]
rs13393021	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13393122	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13425170	0.82[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap]
rs17270233	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17806204	0.82[CEU][hapmap]
rs2288193	0.90[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs2432946	0.81[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs2432956	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2432957	0.81[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs2444264	0.81[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs3771901	1.00[ASW][hapmap];0.91[CEU][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4592848	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs4664490	0.89[ASW][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4664491	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs6718372	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs6724796	1.00[CEU][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6731486	1.00[CEU][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6750342	0.89[ASW][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap]
rs7557092	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602715	0.82[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs9750942	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3693428	chr2:152320932-152434896	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv1793381	chr2:152370040-152463631	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv10198	chr2:152370068-152463644	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv2974	chr2:152401495-152499455	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv469804	chr2:152404429-152570882	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv482520	chr2:152404429-152570882	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4461258	SNORA49	trans	parietal	SCAN
rs4461258	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs4461258	RIF1	cis	parietal	SCAN
rs4461258	RND3	cis	parietal	SCAN
rs4461258	RIF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152409400-152437000	Weak transcription	Psoas Muscle	Psoas
2	chr2:152416200-152434400	Strong transcription	Fetal Muscle Leg	muscle
3	chr2:152427000-152433800	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:152427200-152429800	Weak transcription	HSMMtube	muscle
5	chr2:152427400-152433600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:152429000-152433400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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