Variant report

Variant	rs2808018
Chromosome Location	chr1:220444675-220444676
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr1:220444541-220446530	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:220443180-220446565	GM12891	blood:	n/a	n/a
3	MXI1	chr1:220444039-220446700	SK-N-SH	brain:	n/a	chr1:220445886-220445895
4	REST	chr1:220444642-220446680	H1-neurons	neurons:	n/a	chr1:220445467-220445480 chr1:220445854-220445867 chr1:220444644-220444651 chr1:220445854-220445867
5	ZMIZ1	chr1:220444618-220446473	K562	blood:	n/a	n/a
6	JUN	chr1:220443617-220447007	K562	blood:	n/a	chr1:220444866-220444875 chr1:220445240-220445252
7	POLR2A	chr1:220443457-220446239	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:220443810-220446621	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:220444462-220446119	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220440528..220443413-chr1:220443546..220445862,4	MCF-7	breast:
2	chr1:220443657..220445570-chr1:220960265..220962335,2	MCF-7	breast:

Variant related genes	Relation type
AURKAPS1	TF binding region
ENSG00000213033	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10863537	0.82[JPT][hapmap];0.95[YRI][hapmap]
rs10863538	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11118507	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026681	0.95[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs1397958	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1588578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2221833	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667967	0.92[EUR][1000 genomes]
rs2667968	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667969	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667970	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808008	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808009	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808011	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808019	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2814492	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2814494	0.87[AMR][1000 genomes]
rs2814495	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4142940	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4511114	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6541127	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696985	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7535619	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2808018	MOSC2	cis	lymphoblastoid	seeQTL
rs2808018	C1orf115	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220426800-220445000	Weak transcription	Aorta	Aorta
2	chr1:220426800-220445000	Weak transcription	Pancreas	Pancrea
3	chr1:220427000-220445000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:220434800-220444800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:220439400-220444800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:220441800-220444800	Enhancers	Small Intestine	intestine
7	chr1:220442000-220444800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:220442600-220444800	Enhancers	Liver	Liver
9	chr1:220443200-220444800	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:220443200-220444800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:220443200-220445000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:220443400-220444800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:220443400-220444800	Enhancers	Ovary	ovary
14	chr1:220443400-220444800	Enhancers	Psoas Muscle	Psoas
15	chr1:220443400-220444800	Enhancers	Right Atrium	heart
16	chr1:220443400-220445000	Enhancers	Spleen	Spleen
17	chr1:220443600-220444800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:220443600-220444800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr1:220443600-220444800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:220443600-220445000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:220443600-220445000	Weak transcription	Left Ventricle	heart
22	chr1:220443600-220445000	Weak transcription	Lung	lung
23	chr1:220443600-220446600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:220443800-220445000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr1:220443800-220445200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr1:220443800-220446000	Active TSS	GM12878-XiMat	blood
27	chr1:220443800-220446600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr1:220444000-220444800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:220444000-220444800	Enhancers	Fetal Thymus	thymus
30	chr1:220444000-220444800	Flanking Active TSS	NHEK	skin
31	chr1:220444000-220445000	Enhancers	Gastric	stomach
32	chr1:220444000-220445000	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:220444000-220445200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:220444000-220445200	Flanking Active TSS	Fetal Brain Male	brain
35	chr1:220444000-220445400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr1:220444000-220445600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:220444000-220446000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr1:220444000-220446600	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:220444000-220446600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:220444200-220444800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:220444200-220444800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:220444200-220444800	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr1:220444200-220444800	Enhancers	Brain Substantia Nigra	brain
44	chr1:220444200-220444800	Enhancers	Placenta	Placenta
45	chr1:220444200-220445000	Enhancers	Esophagus	oesophagus
46	chr1:220444200-220445200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:220444200-220445200	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr1:220444200-220445200	Flanking Active TSS	HUVEC	blood vessel
49	chr1:220444200-220445200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr1:220444200-220445400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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