Variant report

Variant	rs11161573
Chromosome Location	chr1:85724581-85724582
allele	A/G
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
ENSG00000142867	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000223254	Chromatin interaction
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10747317	0.89[CHB][hapmap];0.81[GIH][hapmap]
rs10782542	0.89[CHB][hapmap]
rs10782543	0.89[CHB][hapmap];0.81[GIH][hapmap]
rs11161566	0.86[YRI][hapmap]
rs11161568	0.87[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs11161571	0.86[AFR][1000 genomes]
rs11161585	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs11161586	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11161588	1.00[CHB][hapmap]
rs11161592	1.00[CHB][hapmap]
rs11576939	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11580090	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11583827	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11587512	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs11590047	0.81[ASN][1000 genomes]
rs12061512	0.95[ASN][1000 genomes]
rs12084253	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12093484	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs12143140	0.91[AFR][1000 genomes]
rs12403960	0.89[ASN][1000 genomes]
rs12405767	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs12754032	0.81[ASN][1000 genomes]
rs17125445	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs34743622	0.81[ASN][1000 genomes]
rs4949927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4949928	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55808228	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60325409	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668948	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6670921	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs7554249	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs9432848	0.89[CHB][hapmap];0.81[GIH][hapmap]

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
rs11161573	C1orf52	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85710800-85724600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:85722600-85724600	Enhancers	Small Intestine	intestine
3	chr1:85723400-85724600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
4	chr1:85723400-85724600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:85723400-85725600	Active TSS	GM12878-XiMat	blood
6	chr1:85723400-85725800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:85723600-85724800	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr1:85723600-85724800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:85723600-85725400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:85723800-85724600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
11	chr1:85723800-85724600	Flanking Active TSS	Fetal Brain Male	brain
12	chr1:85723800-85724600	Flanking Active TSS	Fetal Brain Female	brain
13	chr1:85723800-85724800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:85723800-85724800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:85723800-85726000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:85723800-85726000	Active TSS	A549	lung
17	chr1:85724000-85724600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:85724000-85724600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:85724000-85724600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:85724000-85724600	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr1:85724000-85724600	Flanking Active TSS	Fetal Stomach	stomach
22	chr1:85724000-85724600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr1:85724000-85724600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr1:85724000-85724600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:85724000-85724600	Enhancers	Spleen	Spleen
26	chr1:85724000-85724600	Flanking Active TSS	Hela-S3	cervix
27	chr1:85724000-85724600	Flanking Active TSS	HUVEC	blood vessel
28	chr1:85724000-85724800	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr1:85724000-85724800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:85724000-85724800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:85724000-85724800	Flanking Active TSS	Liver	Liver
32	chr1:85724000-85725000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr1:85724000-85725400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:85724000-85725400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:85724000-85725600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:85724000-85725600	Active TSS	Thymus	Thymus
37	chr1:85724000-85725600	Active TSS	HSMMtube	muscle
38	chr1:85724000-85725800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:85724000-85725800	Active TSS	Ovary	ovary
40	chr1:85724000-85725800	Active TSS	Right Ventricle	heart
41	chr1:85724000-85726000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:85724000-85726000	Active TSS	Psoas Muscle	Psoas
43	chr1:85724000-85726200	Active TSS	Right Atrium	heart
44	chr1:85724200-85724600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:85724200-85724600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:85724200-85724600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr1:85724200-85724600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:85724200-85724600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:85724200-85724600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:85724200-85724600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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