Variant report

Variant	rs2041318
Chromosome Location	chr5:126438360-126438361
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	chr5:126431823..126435408-chr5:126435480..126438408,3	MCF-7	breast:
2	chr5:126408039..126410323-chr5:126436607..126438479,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164241	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10035217	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10037625	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10038644	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10041457	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1004500	0.89[EUR][1000 genomes]
rs10053382	0.85[CEU][hapmap]
rs10057084	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs10060747	0.85[CEU][hapmap]
rs10062622	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10065302	0.85[CEU][hapmap]
rs10067364	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs10071669	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs1013662	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs1034844	0.85[CEU][hapmap]
rs10491284	0.85[CEU][hapmap];0.81[CHB][hapmap];0.80[TSI][hapmap]
rs10900789	0.81[CEU][hapmap]
rs11949302	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs11956061	0.81[CEU][hapmap]
rs11960799	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs12515192	0.85[CEU][hapmap]
rs12655640	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs12657369	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs13154281	0.84[EUR][1000 genomes]
rs13178353	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13190493	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543815	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs173555	0.90[EUR][1000 genomes]
rs1860439	0.90[EUR][1000 genomes]
rs1860440	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860441	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs193712	0.88[EUR][1000 genomes]
rs2109215	0.82[CEU][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2191209	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240527	0.85[CEU][hapmap]
rs2240528	0.85[CEU][hapmap]
rs2408788	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2408789	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2408790	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2436437	0.90[EUR][1000 genomes]
rs248040	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs248042	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs248062	0.81[EUR][1000 genomes]
rs248081	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs248091	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs248092	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs248093	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs248094	0.91[EUR][1000 genomes]
rs248095	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs248096	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs248101	0.84[EUR][1000 genomes]
rs248102	0.85[EUR][1000 genomes]
rs248104	0.86[EUR][1000 genomes]
rs248106	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs248107	0.96[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs248108	0.85[EUR][1000 genomes]
rs248111	0.91[EUR][1000 genomes]
rs248112	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs248113	0.81[CEU][hapmap]
rs248114	0.90[EUR][1000 genomes]
rs248115	0.90[EUR][1000 genomes]
rs248116	0.87[EUR][1000 genomes]
rs248117	0.89[EUR][1000 genomes]
rs248119	0.90[EUR][1000 genomes]
rs248122	0.90[EUR][1000 genomes]
rs248124	0.90[EUR][1000 genomes]
rs248125	0.90[EUR][1000 genomes]
rs248127	0.90[EUR][1000 genomes]
rs248128	0.90[EUR][1000 genomes]
rs248129	0.90[EUR][1000 genomes]
rs248131	0.90[EUR][1000 genomes]
rs2532882	0.90[EUR][1000 genomes]
rs2898037	0.85[EUR][1000 genomes]
rs3095137	0.90[EUR][1000 genomes]
rs3097870	0.90[EUR][1000 genomes]
rs3915634	0.88[EUR][1000 genomes]
rs3936304	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3936305	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4131248	0.81[CEU][hapmap]
rs4455612	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4835921	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs4835922	0.86[EUR][1000 genomes]
rs4835925	0.90[EUR][1000 genomes]
rs4836307	0.85[CEU][hapmap]
rs4836310	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4836313	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4836315	0.90[EUR][1000 genomes]
rs62374042	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6859962	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6860726	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs6864668	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6873502	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6875043	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6879393	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6881948	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6883106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6883627	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6883672	0.84[EUR][1000 genomes]
rs6883871	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs6884988	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6887929	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6888087	0.90[EUR][1000 genomes]
rs6891436	0.85[CEU][hapmap]
rs6898415	0.80[EUR][1000 genomes]
rs6899133	0.81[EUR][1000 genomes]
rs727038	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs729607	0.85[CEU][hapmap]
rs7700812	0.90[EUR][1000 genomes]
rs7706333	0.85[CEU][hapmap]
rs7713933	0.81[CEU][hapmap];0.90[CHB][hapmap];0.80[TSI][hapmap]
rs7731621	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7733551	0.85[CEU][hapmap]
rs7734890	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7736693	0.85[CEU][hapmap]
rs885699	0.90[EUR][1000 genomes]
rs9327428	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[TSI][hapmap]
rs9687751	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9687752	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9763733	0.88[EUR][1000 genomes]
rs990743	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1816248	chr5:126399039-126486539	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2041318	C5orf63	cis	Nerve Tibial	GTEx
rs2041318	C5orf63	cis	Artery Tibial	GTEx
rs2041318	MARCH3	cis	parietal	SCAN
rs2041318	MARCH3	cis	cerebellum	SCAN
rs2041318	MARCH3	cis	Muscle Skeletal	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126433400-126444200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:126435800-126438400	Enhancers	Fetal Intestine Small	intestine

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