Variant report

Variant	rs4949926
Chromosome Location	chr1:85724328-85724329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85666179..85667836-chr1:85723614..85725791,2	K562	blood:
2	chr1:85722628..85726570-chr1:85740869..85744448,4	MCF-7	breast:
3	chr1:85724038..85728124-chr1:85728267..85730109,3	K562	blood:
4	chr1:85723982..85727421-chr1:85728589..85731374,3	MCF-7	breast:
5	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
6	chr1:85664620..85668785-chr1:85722586..85726821,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223254	Chromatin interaction
ENSG00000142867	Chromatin interaction
ENSG00000097096	Chromatin interaction
ENSG00000223653	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11161556	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161574	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161584	0.93[EUR][1000 genomes]
rs11577656	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11583836	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12065422	0.82[EUR][1000 genomes]
rs12563295	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17123650	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2252408	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2647396	0.90[ASN][1000 genomes]
rs2735587	0.85[ASN][1000 genomes]
rs2735588	0.87[ASN][1000 genomes]
rs2735591	0.87[ASN][1000 genomes]
rs2735592	0.88[ASN][1000 genomes]
rs2735593	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2735594	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36006436	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4949892	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60156243	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6663690	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6671589	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6693365	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72722624	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72722631	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72722638	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72722641	0.83[ASN][1000 genomes]
rs72722643	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][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
rs4949926	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85707800-85724400	Weak transcription	Lung	lung
2	chr1:85710800-85724400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:85710800-85724600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:85720200-85724400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:85722600-85724600	Enhancers	Small Intestine	intestine
6	chr1:85722800-85724400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:85723000-85724400	Enhancers	Stomach Mucosa	stomach
8	chr1:85723000-85724400	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr1:85723200-85724400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
10	chr1:85723400-85724600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
11	chr1:85723400-85724600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:85723400-85725600	Active TSS	GM12878-XiMat	blood
13	chr1:85723400-85725800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:85723600-85724800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:85723600-85724800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:85723600-85725400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:85723800-85724400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
18	chr1:85723800-85724400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
19	chr1:85723800-85724400	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr1:85723800-85724400	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr1:85723800-85724400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
22	chr1:85723800-85724400	Transcr. at gene 5' and 3'	HSMM	muscle
23	chr1:85723800-85724400	Transcr. at gene 5' and 3'	K562	blood
24	chr1:85723800-85724400	Flanking Active TSS	NHLF	lung
25	chr1:85723800-85724600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
26	chr1:85723800-85724600	Flanking Active TSS	Fetal Brain Male	brain
27	chr1:85723800-85724600	Flanking Active TSS	Fetal Brain Female	brain
28	chr1:85723800-85724800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:85723800-85724800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr1:85723800-85726000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:85723800-85726000	Active TSS	A549	lung
32	chr1:85724000-85724400	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
33	chr1:85724000-85724400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:85724000-85724400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:85724000-85724400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:85724000-85724400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
37	chr1:85724000-85724400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:85724000-85724400	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr1:85724000-85724400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:85724000-85724400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:85724000-85724400	Flanking Active TSS	Fetal Heart	heart
42	chr1:85724000-85724400	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr1:85724000-85724400	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
44	chr1:85724000-85724400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr1:85724000-85724400	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
46	chr1:85724000-85724400	Flanking Active TSS	HepG2	liver
47	chr1:85724000-85724400	Transcr. at gene 5' and 3'	NHEK	skin
48	chr1:85724000-85724600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:85724000-85724600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr1:85724000-85724600	Flanking Active TSS	Adipose Nuclei	Adipose

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