Variant report

Variant	rs12037201
Chromosome Location	chr1:45941349-45941350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45936186..45938090-chr1:45940024..45942572,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1006216	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1007858	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10789464	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1084166	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10890327	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890330	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211101	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211108	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211111	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211117	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211118	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211123	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211124	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11211128	0.84[AMR][1000 genomes]
rs12029322	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12037411	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12042903	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12046816	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12066142	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067642	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12097497	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12410493	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564806	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1417578	0.87[EUR][1000 genomes]
rs1494812	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17395553	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771551	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1826691	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2050884	0.87[EUR][1000 genomes]
rs2055145	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2088100	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2153607	0.83[EUR][1000 genomes]
rs2153608	0.83[EUR][1000 genomes]
rs2153609	0.84[EUR][1000 genomes]
rs2185549	0.83[EUR][1000 genomes]
rs2298018	0.83[EUR][1000 genomes]
rs2487442	0.89[EUR][1000 genomes]
rs2492836	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2492840	0.87[EUR][1000 genomes]
rs28555082	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3219463	0.82[EUR][1000 genomes]
rs3219472	0.82[EUR][1000 genomes]
rs34673142	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3790582	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3790583	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4633317	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4660301	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660849	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660851	0.86[EUR][1000 genomes]
rs4660852	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660853	0.86[EUR][1000 genomes]
rs4660854	0.87[EUR][1000 genomes]
rs4660855	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660858	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4660863	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5015340	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55642258	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61788261	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61788262	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61788281	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61788285	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61788336	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61791362	0.86[EUR][1000 genomes]
rs61791368	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61791369	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67683090	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs713358	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7417107	0.87[EUR][1000 genomes]
rs7528573	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7531253	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532762	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7543428	0.86[EUR][1000 genomes]
rs7544178	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553318	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs781226	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs781230	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs781232	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs884962	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9326141	0.86[EUR][1000 genomes];0.84[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	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9429160	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9429161	0.86[EUR][1000 genomes]
rs9727262	0.82[AMR][1000 genomes]
rs9729395	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
7	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
8	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
9	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12037201	C2orf49	trans	lymphoblastoid	RTeQTL
rs12037201	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs12037201	MMACHC	cis	multi-tissue	Pritchard
rs12037201	TESK2	cis	Whole Blood	GTEx
rs12037201	PRDX1	cis	Thyroid	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45923600-45951600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:45935600-45943400	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:45936400-45943800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:45939400-45943400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:45939400-45955000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:45939600-45943400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:45940200-45944200	Weak transcription	Liver	Liver
8	chr1:45941200-45941600	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:45941200-45942200	Genic enhancers	Fetal Intestine Small	intestine
10	chr1:45941200-45944800	Weak transcription	GM12878-XiMat	blood
11	chr1:45941200-45955000	Weak transcription	Primary B cells from peripheral blood	blood

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