Variant report

Variant	rs61791368
Chromosome Location	chr1:45867944-45867945
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	chr1:45867610..45870070-chr1:45874178..45875869,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1006216	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1007858	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1084166	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10890327	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10890330	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11211101	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211108	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211111	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211117	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211118	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12037201	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12037411	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046816	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12067642	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12097497	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12410493	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12564806	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1417578	0.87[EUR][1000 genomes]
rs1494812	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17395553	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1771551	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1826691	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2050884	0.87[EUR][1000 genomes]
rs2055145	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2088100	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153607	0.83[EUR][1000 genomes]
rs2153608	0.83[EUR][1000 genomes]
rs2153609	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2185549	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2298018	0.83[EUR][1000 genomes]
rs2487442	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2492836	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2492840	0.87[EUR][1000 genomes]
rs28555082	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3219463	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3219472	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3219489	0.81[EUR][1000 genomes]
rs3790582	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660301	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660849	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4660851	0.88[EUR][1000 genomes]
rs4660852	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660853	0.88[EUR][1000 genomes]
rs4660854	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4660855	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4660858	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55642258	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61788261	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61788262	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61788281	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61788285	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61791362	0.83[EUR][1000 genomes]
rs61791369	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72686460	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7417107	0.87[EUR][1000 genomes]
rs7525849	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7528573	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7531253	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7532762	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7536135	0.81[EUR][1000 genomes]
rs7543428	0.88[EUR][1000 genomes]
rs7544178	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7553318	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs781226	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs781230	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs781232	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs884962	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9326141	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9429072	0.83[EUR][1000 genomes]
rs9429074	0.83[EUR][1000 genomes]
rs9429076	0.84[EUR][1000 genomes]
rs9429158	0.85[EUR][1000 genomes]
rs9429159	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9429160	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9429161	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61791368	MMACHC	cis	multi-tissue	Pritchard
rs61791368	TESK2	cis	Whole Blood	GTEx
rs61791368	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45841400-45889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45860200-45869000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:45860200-45869800	Weak transcription	Brain Anterior Caudate	brain
4	chr1:45861000-45869200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:45861200-45874600	Weak transcription	GM12878-XiMat	blood
6	chr1:45865800-45869400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:45867000-45868000	Enhancers	HepG2	liver
8	chr1:45867000-45870200	Enhancers	Liver	Liver
9	chr1:45867200-45868200	Enhancers	Fetal Intestine Large	intestine
10	chr1:45867200-45869400	Enhancers	Fetal Intestine Small	intestine
11	chr1:45867400-45868000	Enhancers	Small Intestine	intestine
12	chr1:45867800-45868000	Enhancers	Esophagus	oesophagus

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