Variant report

Variant	rs2808019
Chromosome Location	chr1:220444925-220444926
allele	A/G
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	POLR2A	chr1:220444744-220446443	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBL1XR1	chr1:220444857-220445410	K562	blood:	n/a	n/a
3	POLR2A	chr1:220444840-220446403	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:220444876-220446303	GM12878	blood:	n/a	n/a
5	RUNX3	chr1:220444840-220445358	GM12878	blood:	n/a	n/a
6	STAT5A	chr1:220444817-220446222	GM12878	blood:	n/a	chr1:220445273-220445285
7	POLR2A	chr1:220444909-220446477	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:220444777-220446366	MCF10A-Er-Src	breast:	n/a	n/a
9	HCFC1	chr1:220444541-220446530	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:220443180-220446565	GM12891	blood:	n/a	n/a
11	UBTF	chr1:220444896-220446202	K562	blood:	n/a	n/a
12	MYC	chr1:220444904-220446266	K562	blood:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
13	YY1	chr1:220444920-220445185	GM12878	blood:	n/a	n/a
14	MAZ	chr1:220444884-220446234	GM12878	blood:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
15	MXI1	chr1:220444039-220446700	SK-N-SH	brain:	n/a	chr1:220445886-220445895
16	REST	chr1:220444642-220446680	H1-neurons	neurons:	n/a	chr1:220445467-220445480 chr1:220445854-220445867 chr1:220444644-220444651 chr1:220445854-220445867
17	MAFK	chr1:220444843-220445036	K562	blood:	n/a	n/a
18	POLR2A	chr1:220444835-220446268	GM12892	blood:	n/a	n/a
19	YY1	chr1:220444910-220446119	GM12892	blood:	n/a	chr1:220445899-220445908
20	JUND	chr1:220444853-220446465	K562	blood:	n/a	chr1:220444866-220444875 chr1:220445240-220445252
21	POLR2A	chr1:220444714-220446272	GM12892	blood:	n/a	n/a
22	MAX	chr1:220444919-220446357	H1-hESC	embryonic stem cell:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
23	POLR2A	chr1:220444912-220446437	PBDE	blood:	n/a	n/a
24	TCF12	chr1:220444806-220446356	A549	lung:	n/a	n/a
25	POLR2A	chr1:220444882-220446502	GM19099	blood:	n/a	n/a
26	ZMIZ1	chr1:220444618-220446473	K562	blood:	n/a	n/a
27	JUN	chr1:220443617-220447007	K562	blood:	n/a	chr1:220444866-220444875 chr1:220445240-220445252
28	POLR2A	chr1:220443457-220446239	GM12878	blood:	n/a	n/a
29	YY1	chr1:220444877-220445391	H1-hESC	embryonic stem cell:	n/a	n/a
30	SIN3A	chr1:220444906-220446463	H1-hESC	embryonic stem cell:	n/a	chr1:220445888-220445897 chr1:220445886-220445895
31	MAX	chr1:220444873-220446408	A549	lung:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
32	MAX	chr1:220444908-220446323	HepG2	liver:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
33	STAT3	chr1:220444863-220445030	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr1:220443810-220446621	MCF10A-Er-Src	breast:	n/a	n/a
35	PML	chr1:220444860-220446364	GM12878	blood:	n/a	chr1:220445246-220445254
36	MTA3	chr1:220444744-220446574	GM12878	blood:	n/a	n/a
37	CUX1	chr1:220444890-220445048	K562	blood:	n/a	n/a
38	POLR2A	chr1:220444908-220446150	K562	blood:	n/a	n/a
39	TEAD4	chr1:220444764-220446539	K562	blood:	n/a	chr1:220445255-220445264
40	MYC	chr1:220444751-220445235	MCF10A-Er-Src	breast:	n/a	n/a
41	TAF1	chr1:220444881-220446352	H1-neurons	neurons:	n/a	n/a
42	MAX	chr1:220444854-220446324	HCT-116	colon:	n/a	chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445887-220445896 chr1:220445515-220445525 chr1:220445887-220445896 chr1:220445885-220445898 chr1:220445882-220445901
43	NR2F2	chr1:220444815-220446346	K562	blood:	n/a	n/a
44	POLR2A	chr1:220444462-220446119	IMR90	lung:	n/a	n/a
45	YY1	chr1:220444827-220445231	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220444920..220445420-chr17:75491133..75491675,2	MCF-7	breast:
2	chr1:220440528..220443413-chr1:220443546..220445862,4	MCF-7	breast:
3	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	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11118507	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12026681	0.95[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs1397958	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1588578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2221833	0.89[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	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667969	0.82[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	0.89[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];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2808011	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808012	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808013	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2808018	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	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2814494	0.87[AMR][1000 genomes]
rs2814495	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4142940	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4511114	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6541127	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696985	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7535619	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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
rs2808019	MOSC2	cis	lymphoblastoid	seeQTL
rs2808019	C1orf115	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 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	chr1:220443200-220445000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:220443400-220445000	Enhancers	Spleen	Spleen
6	chr1:220443600-220445000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:220443600-220445000	Weak transcription	Left Ventricle	heart
8	chr1:220443600-220445000	Weak transcription	Lung	lung
9	chr1:220443600-220446600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:220443800-220445000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:220443800-220445200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr1:220443800-220446000	Active TSS	GM12878-XiMat	blood
13	chr1:220443800-220446600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr1:220444000-220445000	Enhancers	Gastric	stomach
15	chr1:220444000-220445000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:220444000-220445200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:220444000-220445200	Flanking Active TSS	Fetal Brain Male	brain
18	chr1:220444000-220445400	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr1:220444000-220445600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:220444000-220446000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr1:220444000-220446600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr1:220444000-220446600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:220444200-220445000	Enhancers	Esophagus	oesophagus
24	chr1:220444200-220445200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:220444200-220445200	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr1:220444200-220445200	Flanking Active TSS	HUVEC	blood vessel
27	chr1:220444200-220445200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr1:220444200-220445400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr1:220444200-220446200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:220444200-220446400	Active TSS	HSMMtube	muscle
31	chr1:220444200-220446600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr1:220444400-220445000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:220444400-220445000	Active TSS	HepG2	liver
34	chr1:220444400-220445200	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr1:220444400-220445200	Flanking Active TSS	Dnd41	blood
36	chr1:220444400-220445400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:220444400-220446200	Active TSS	Primary T cells fromperipheralblood	blood
38	chr1:220444400-220446400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:220444400-220446400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:220444400-220446400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:220444400-220446400	Active TSS	Colonic Mucosa	Colon
42	chr1:220444400-220446400	Active TSS	Fetal Intestine Small	intestine
43	chr1:220444400-220446600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:220444400-220446600	Active TSS	Brain Angular Gyrus	brain
45	chr1:220444600-220445000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:220444600-220445000	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr1:220444600-220445200	Flanking Active TSS	Fetal Stomach	stomach
48	chr1:220444600-220445600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr1:220444600-220446000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr1:220444600-220446000	Active TSS	HUES6 Cell Line	embryonic stem cell

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