Variant report

Variant	rs2252408
Chromosome Location	chr1:85733929-85733930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85731843..85735394-chr1:85740314..85743094,4	MCF-7	breast:
2	chr1:85405508..85407651-chr1:85733535..85736514,2	K562	blood:
3	chr1:85730097..85732831-chr1:85733778..85736278,2	K562	blood:

Variant related genes	Relation type
ENSG00000223653	Chromatin interaction
ENSG00000142867	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11161556	0.92[EUR][1000 genomes]
rs11161574	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11161584	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11577656	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11583836	0.91[EUR][1000 genomes]
rs12065422	0.80[EUR][1000 genomes]
rs12563295	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17123650	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2647396	0.99[ASN][1000 genomes]
rs2735587	0.94[ASN][1000 genomes]
rs2735588	0.89[ASN][1000 genomes]
rs2735591	0.96[ASN][1000 genomes]
rs2735592	0.97[ASN][1000 genomes]
rs2735593	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735594	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36006436	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949892	0.93[EUR][1000 genomes]
rs4949926	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60156243	0.93[EUR][1000 genomes]
rs6663690	0.93[EUR][1000 genomes]
rs6671589	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6693365	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72722624	0.88[EUR][1000 genomes]
rs72722631	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72722638	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72722643	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252408	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85725400-85734600	Weak transcription	Small Intestine	intestine
2	chr1:85725400-85741000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:85725600-85734600	Weak transcription	Lung	lung
4	chr1:85725600-85737000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:85725800-85734600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:85725800-85734600	Weak transcription	Esophagus	oesophagus
7	chr1:85725800-85734800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:85725800-85739400	Weak transcription	Aorta	Aorta
9	chr1:85726000-85734000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:85726000-85734000	Weak transcription	Ovary	ovary
11	chr1:85726000-85734200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:85726000-85734400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:85726000-85734400	Weak transcription	Fetal Heart	heart
14	chr1:85726000-85734400	Weak transcription	HepG2	liver
15	chr1:85726000-85734600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:85726000-85734600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:85726000-85734600	Weak transcription	Fetal Brain Male	brain
18	chr1:85726000-85734600	Weak transcription	Right Ventricle	heart
19	chr1:85726000-85734800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:85726000-85741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:85726000-85741400	Weak transcription	Gastric	stomach
22	chr1:85726200-85734600	Weak transcription	Fetal Brain Female	brain
23	chr1:85726200-85735200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:85726200-85739800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:85726600-85734600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:85727200-85741400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:85727800-85737400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:85728000-85737400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:85728200-85739400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:85728400-85738400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:85728600-85734600	Weak transcription	Pancreas	Pancrea
32	chr1:85728600-85738800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:85728600-85739600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:85728600-85739600	Strong transcription	HSMM	muscle
35	chr1:85728800-85734600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:85728800-85739000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:85728800-85739000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:85728800-85739600	Strong transcription	Primary hematopoietic stem cells	blood
39	chr1:85729000-85735200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:85729000-85739200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:85729200-85734600	Strong transcription	Dnd41	blood
42	chr1:85729200-85737800	Strong transcription	Placenta	Placenta
43	chr1:85729200-85738000	Strong transcription	Fetal Thymus	thymus
44	chr1:85729200-85738400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:85729200-85738800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:85729200-85739400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:85729200-85739600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:85729400-85738000	Strong transcription	Primary B cells from cord blood	blood
49	chr1:85729400-85739200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr1:85729600-85737000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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