Variant report

Variant	rs12564806
Chromosome Location	chr1:45924230-45924231
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	chr1:45923357..45924859-chr1:45987046..45988646,2	K562	blood:
2	chr1:45923646..45925304-chr1:45931441..45933982,2	K562	blood:

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1006216	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1007858	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10789464	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1084166	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10890327	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10890330	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211101	0.81[EUR][1000 genomes]
rs11211108	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211111	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11211117	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211118	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211123	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211124	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11211128	0.80[EUR][1000 genomes]
rs12029322	0.86[EUR][1000 genomes]
rs12037201	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12037411	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12042903	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12046816	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12066142	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12067642	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12097497	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12410493	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1494812	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17395553	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1771551	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1826691	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2055145	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088100	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2487442	0.81[EUR][1000 genomes]
rs2492836	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28555082	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2883968	0.81[EUR][1000 genomes]
rs34673142	0.85[EUR][1000 genomes]
rs3790582	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790583	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4633317	0.85[EUR][1000 genomes]
rs4660851	0.80[EUR][1000 genomes]
rs4660852	0.81[EUR][1000 genomes]
rs4660853	0.80[EUR][1000 genomes]
rs4660854	0.81[EUR][1000 genomes]
rs4660855	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4660858	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660863	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5015340	0.85[EUR][1000 genomes]
rs55642258	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61788261	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61788262	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61788281	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61788285	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61788336	0.86[EUR][1000 genomes]
rs61791368	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61791369	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67683090	0.85[EUR][1000 genomes]
rs713358	0.85[EUR][1000 genomes]
rs7528573	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7531253	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532762	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7543428	0.80[EUR][1000 genomes]
rs7553318	0.81[EUR][1000 genomes]
rs781226	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs781230	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs781232	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs884962	0.81[EUR][1000 genomes]
rs9326141	0.80[EUR][1000 genomes]
rs9429161	0.80[EUR][1000 genomes]
rs9727262	0.84[EUR][1000 genomes]
rs9729395	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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12564806	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs12564806	PRDX1	cis	Thyroid	GTEx
rs12564806	C2orf49	trans	lymphoblastoid	RTeQTL
rs12564806	TESK2	cis	Whole Blood	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45889800-45940600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:45909000-45924600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:45911000-45930400	Weak transcription	Psoas Muscle	Psoas
4	chr1:45911400-45924400	Weak transcription	Placenta	Placenta
5	chr1:45913000-45931000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:45913000-45933000	Weak transcription	Ovary	ovary
7	chr1:45915400-45924800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:45915400-45940600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:45915600-45929600	Weak transcription	Left Ventricle	heart
10	chr1:45917000-45930000	Weak transcription	Aorta	Aorta
11	chr1:45919000-45941000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:45920600-45932600	Weak transcription	GM12878-XiMat	blood
13	chr1:45921200-45924600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:45921200-45924600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:45921200-45924600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:45921200-45933800	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:45921200-45934200	Weak transcription	Brain Substantia Nigra	brain
18	chr1:45921400-45924800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:45921800-45933000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:45923400-45928000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:45923400-45940600	Weak transcription	Primary B cells from cord blood	blood
22	chr1:45923600-45951600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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