Variant report

Variant	rs478093
Chromosome Location	chr1:120255126-120255127
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120229496..120231621-chr1:120254696..120256885,2	K562	blood:
2	chr1:120188760..120191651-chr1:120254416..120257641,3	K562	blood:
3	chr1:120254449..120255374-chr3:25705936..25706569,2	Hela-S3	cervix:
4	chr1:120188760..120191459-chr1:120254916..120257641,2	K562	blood:
5	chr1:120253275..120257099-chr1:120276679..120281090,4	K562	blood:
6	chr1:120186762..120190857-chr1:120254727..120257522,5	MCF-7	breast:
7	chr1:120254553..120256088-chr2:64878581..64881512,2	K562	blood:
8	chr1:120201333..120204049-chr1:120254351..120256217,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction
ENSG00000092621	Chromatin interaction
ENSG00000179833	Chromatin interaction
ENSG00000264219	Chromatin interaction
ENSG00000077097	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1163251	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2764886	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs477992	0.91[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs483180	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs487081	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs487884	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs496195	0.85[ASN][1000 genomes]
rs496198	0.85[ASN][1000 genomes]
rs511059	0.88[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs514491	0.85[ASN][1000 genomes]
rs517533	0.85[ASN][1000 genomes]
rs532303	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs539708	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs541503	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs561931	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs592762	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs594400	0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs595283	0.93[ASN][1000 genomes]
rs597308	0.85[ASN][1000 genomes]
rs598685	0.85[ASN][1000 genomes]
rs606312	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs611365	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs612430	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs627707	0.88[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs629735	0.88[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs637868	0.86[JPT][hapmap]
rs639216	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs639761	0.87[ASN][1000 genomes]
rs640195	0.87[ASN][1000 genomes]
rs658442	0.89[ASN][1000 genomes]
rs660073	0.89[ASN][1000 genomes]
rs662243	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs662602	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs666930	0.86[JPT][hapmap]
rs677277	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs839600	0.85[ASN][1000 genomes]
rs839605	0.88[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs866321	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS 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 target site	38 gene(s)	inside rSNPs	diseases
5	esv3417273	chr1:120254479-120256427	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Metabolite levels	23378610	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs478093	C1orf161	cis	parietal	SCAN
rs478093	PHGDH	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120254200-120255200	Active TSS	Primary T helper naive cells from peripheral blood	blood
2	chr1:120254200-120255200	Bivalent/Poised TSS	HepG2	liver
3	chr1:120254200-120255200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:120254200-120255400	Active TSS	Primary T cells from cord blood	blood
5	chr1:120254200-120255400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:120254200-120255400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:120254200-120255400	Active TSS	Brain Cingulate Gyrus	brain
8	chr1:120254200-120255400	Active TSS	A549	lung
9	chr1:120254200-120255600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:120254200-120255600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:120254200-120255600	Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr1:120254200-120255600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:120254200-120255600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr1:120254200-120255600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:120254200-120255600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:120254200-120255600	Active TSS	Brain Germinal Matrix	brain
17	chr1:120254200-120255600	Active TSS	Fetal Brain Female	brain
18	chr1:120254200-120255600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:120254200-120255600	Active TSS	Fetal Lung	lung
20	chr1:120254200-120255600	Active TSS	Fetal Stomach	stomach
21	chr1:120254200-120255600	Active TSS	Thymus	Thymus
22	chr1:120254200-120255600	Active TSS	HSMM	muscle
23	chr1:120254200-120255600	Active TSS	NH-A	brain
24	chr1:120254200-120255600	Active TSS	Osteobl	bone
25	chr1:120254200-120255800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:120254200-120255800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:120254200-120255800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:120254200-120255800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:120254200-120255800	Active TSS	Aorta	Aorta
30	chr1:120254200-120255800	Active TSS	Brain Hippocampus Middle	brain
31	chr1:120254200-120255800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr1:120254200-120255800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:120254200-120255800	Active TSS	Colon Smooth Muscle	Colon
34	chr1:120254200-120255800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr1:120254200-120255800	Active TSS	Fetal Intestine Large	intestine
36	chr1:120254200-120255800	Active TSS	Fetal Kidney	kidney
37	chr1:120254200-120255800	Active TSS	Ovary	ovary
38	chr1:120254200-120255800	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:120254200-120255800	Active TSS	NHLF	lung
40	chr1:120254200-120256000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:120254200-120256000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr1:120254200-120256000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:120254200-120256000	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr1:120254200-120256000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:120254200-120256000	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr1:120254200-120256000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:120254200-120256000	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:120254200-120256000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:120254200-120256000	Active TSS	Brain Angular Gyrus	brain
50	chr1:120254200-120256000	Active TSS	Brain Anterior Caudate	brain

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