Variant report

Variant	rs12066142
Chromosome Location	chr1:45963249-45963250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
2	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
3	chr1:45961218..45963399-chr1:45963495..45965607,2	K562	blood:

Variant related genes	Relation type
ENSG00000236624	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000132781	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1006216	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1007858	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789464	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890330	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211111	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11211117	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211118	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211123	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211128	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12029322	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037201	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12042903	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12067642	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12410493	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12564806	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2055145	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28555082	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2883968	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34673142	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3790583	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4633317	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660858	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660863	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5015340	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55642258	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61788261	0.81[EUR][1000 genomes]
rs61788281	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61788285	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61788336	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788356	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67683090	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs713358	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7528573	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs868351	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9727262	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9729395	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][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	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
3	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
4	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
5	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
6	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
7	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
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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	232 gene(s)	inside rSNPs	diseases
9	esv3436377	chr1:45963015-45964113	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12066142	C2orf49	trans	lymphoblastoid	RTeQTL
rs12066142	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs12066142	TESK2	cis	Whole Blood	GTEx
rs12066142	PRDX1	cis	Thyroid	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45964600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:45956800-45964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:45956800-45964800	Weak transcription	Spleen	Spleen
4	chr1:45956800-45965000	Weak transcription	Gastric	stomach
5	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
6	chr1:45957000-45964200	Weak transcription	Pancreas	Pancrea
7	chr1:45957000-45964400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:45957000-45964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:45957000-45964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:45957200-45964200	Weak transcription	K562	blood
11	chr1:45957400-45964000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:45957400-45964600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:45957400-45965200	Weak transcription	HSMM	muscle
14	chr1:45957600-45964000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:45957600-45964000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:45957600-45964200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:45957600-45964200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:45957600-45964200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:45957600-45964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:45957600-45964600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:45957600-45964600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:45957600-45964600	Weak transcription	Ovary	ovary
23	chr1:45957600-45964600	Weak transcription	Thymus	Thymus
24	chr1:45957600-45964600	Weak transcription	Osteobl	bone
25	chr1:45957600-45964800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:45957600-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:45957600-45964800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:45957600-45965000	Weak transcription	Psoas Muscle	Psoas
29	chr1:45957800-45964000	Weak transcription	Liver	Liver
30	chr1:45957800-45964000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:45957800-45964000	Weak transcription	Brain Substantia Nigra	brain
32	chr1:45957800-45964200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:45957800-45964400	Weak transcription	Brain Angular Gyrus	brain
34	chr1:45957800-45964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:45957800-45964600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:45957800-45964600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:45957800-45964800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:45957800-45964800	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:45957800-45965000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:45957800-45965000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:45958000-45964000	Weak transcription	Dnd41	blood
42	chr1:45958000-45964200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:45958000-45964200	Weak transcription	GM12878-XiMat	blood
44	chr1:45958000-45964400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:45958000-45964400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:45958000-45964400	Weak transcription	Fetal Thymus	thymus
47	chr1:45958000-45964400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:45958000-45964600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:45958000-45964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:45958000-45964600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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