Variant report

Variant	rs868494
Chromosome Location	chr1:220959517-220959518
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	HEY1	chr1:220959459-220960459	HepG2	liver:	n/a	n/a
2	HEY1	chr1:220959476-220961035	HepG2	liver:	n/a	n/a
3	MAX	chr1:220959476-220961100	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:220958619-220961999	Hela-S3	cervix:	n/a	n/a
5	KAP1	chr1:220958335-220960481	HEK293	kidney:	n/a	n/a
6	YY1	chr1:220959453-220960995	HepG2	liver:	n/a	chr1:220960128-220960137 chr1:220959814-220959828 chr1:220959704-220959715 chr1:220960582-220960593 chr1:220960125-220960134 chr1:220959735-220959749
7	KAP1	chr1:220959287-220960313	U2OS	brain:	n/a	n/a
8	BACH1	chr1:220959433-220960912	H1-hESC	embryonic stem cell:	n/a	n/a
9	GABPA	chr1:220959469-220959674	HepG2	liver:	n/a	n/a
10	ZEB1	chr1:220959446-220961221	HepG2	liver:	n/a	n/a
11	TAF1	chr1:220959507-220959782	H1-hESC	embryonic stem cell:	n/a	n/a
12	MYBL2	chr1:220959167-220959709	HepG2	liver:	n/a	n/a
13	CTBP2	chr1:220959280-220961075	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:220959476-220961466	HepG2	liver:	n/a	n/a
15	SIN3A	chr1:220959428-220960924	H1-hESC	embryonic stem cell:	n/a	chr1:220959616-220959625 chr1:220960042-220960053
16	JUND	chr1:220959474-220959799	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:220959315-220961191	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr1:220959462-220961098	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr1:220959233-220961100	HepG2	liver:	n/a	n/a
20	SMARCB1	chr1:220959466-220961030	Hela-S3	cervix:	n/a	n/a
21	MAX	chr1:220959409-220961067	H1-hESC	embryonic stem cell:	n/a	n/a
22	TBP	chr1:220959509-220961061	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr1:220959371-220961133	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:220959217-220961067	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220956529..220963831-chr1:220968712..220974793,12	MCF-7	breast:
2	chr1:220920087..220922800-chr1:220958239..220960991,2	MCF-7	breast:
3	chr1:220959343..220960099-chr7:45026038..45026887,2	Hela-S3	cervix:
4	chr1:220958915..220961807-chr1:220964103..220968214,4	MCF-7	breast:
5	chr1:220958940..220961119-chr1:220964763..220966587,2	MCF-7	breast:

Variant related genes	Relation type
MARC1	TF binding region
ENSG00000186205	Chromatin interaction
ENSG00000232956	Chromatin interaction
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11118601	1.00[CEU][hapmap];0.92[AMR][1000 genomes]
rs12028745	1.00[CEU][hapmap]
rs12562744	0.82[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs1690716	0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs3820354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[ASN][1000 genomes]
rs3820356	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57298117	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58327003	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58438675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59234976	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6541159	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6682431	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683301	0.89[ASN][1000 genomes]
rs6701709	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72470566	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72470578	0.94[AMR][1000 genomes]
rs72470579	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72470580	0.94[AMR][1000 genomes]
rs72470582	0.94[AMR][1000 genomes]
rs7526347	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7537305	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9970238	1.00[CEU][hapmap];0.90[AMR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs868494	MOSC2	cis	lymphoblastoid	seeQTL
rs868494	C1orf115	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:220930000-220959600	Weak transcription	Psoas Muscle	Psoas
4	chr1:220930400-220959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:220936200-220959600	Weak transcription	A549	lung
6	chr1:220939000-220960400	Weak transcription	Small Intestine	intestine
7	chr1:220944200-220959600	Weak transcription	NHLF	lung
8	chr1:220944200-220959800	Weak transcription	Gastric	stomach
9	chr1:220953200-220959600	Weak transcription	Lung	lung
10	chr1:220956800-220959600	Enhancers	Hela-S3	cervix
11	chr1:220957000-220959600	Weak transcription	Aorta	Aorta
12	chr1:220958000-220959600	Enhancers	Liver	Liver
13	chr1:220958200-220959800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:220958200-220959800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:220958400-220959600	Weak transcription	Left Ventricle	heart
16	chr1:220958600-220959600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:220958600-220959600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:220958600-220959600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:220958800-220959600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:220959000-220959600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr1:220959000-220959600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr1:220959000-220959600	Enhancers	Brain Substantia Nigra	brain
23	chr1:220959000-220959800	Enhancers	Fetal Heart	heart
24	chr1:220959000-220960200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr1:220959000-220962000	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr1:220959200-220959600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr1:220959200-220959600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:220959200-220959600	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:220959200-220959600	Active TSS	Brain Hippocampus Middle	brain
30	chr1:220959200-220959600	Genic enhancers	Fetal Intestine Small	intestine
31	chr1:220959200-220959600	Enhancers	Ovary	ovary
32	chr1:220959200-220959800	Enhancers	Esophagus	oesophagus
33	chr1:220959200-220959800	Enhancers	Fetal Lung	lung
34	chr1:220959200-220960000	Flanking Active TSS	Fetal Brain Female	brain
35	chr1:220959200-220960000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr1:220959200-220960000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr1:220959200-220960200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:220959200-220962600	Enhancers	Fetal Brain Male	brain
39	chr1:220959400-220959600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr1:220959400-220959600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
41	chr1:220959400-220959600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:220959400-220959600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
43	chr1:220959400-220959600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:220959400-220959600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr1:220959400-220959600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr1:220959400-220959600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr1:220959400-220959600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:220959400-220959600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:220959400-220959600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:220959400-220959600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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