Variant report

Variant	rs2281039
Chromosome Location	chr1:169763229-169763230
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr1:169763137-169764771	K562	blood:	n/a	n/a
2	POLR2A	chr1:169763165-169766289	K562	blood:	n/a	n/a
3	GABPA	chr1:169763184-169764838	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:169763021-169765340	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr1:169763111-169765549	IMR90	lung:	n/a	n/a
6	POLR2A	chr1:169763227-169765745	GM12878	blood:	n/a	n/a
7	HCFC1	chr1:169763085-169765566	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:169763205-169764648	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:169763181-169766127	GM12891	blood:	n/a	n/a
10	MAFK	chr1:169762891-169763264	HepG2	liver:	n/a	n/a
11	MAFK	chr1:169762919-169764387	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:169763143-169765402	K562	blood:	n/a	n/a
13	GTF2F1	chr1:169763189-169764716	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:169763114-169764613	GM12878	blood:	n/a	n/a
15	MAFK	chr1:169762895-169763235	HepG2	liver:	n/a	n/a
16	MYC	chr1:169763210-169764499	K562	blood:	n/a	n/a
17	POLR2A	chr1:169763216-169765108	K562	blood:	n/a	n/a
18	POLR2A	chr1:169763186-169765296	GM18505	blood:	n/a	n/a
19	MAFF	chr1:169762906-169763257	K562	blood:	n/a	chr1:169763065-169763083
20	POLR2A	chr1:169763043-169764894	SK-N-MC	brain:	n/a	n/a
21	MTA3	chr1:169763206-169765978	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:169763200-169764804	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169335832..169338194-chr1:169763167..169765301,2	K562	blood:
2	chr1:169737043..169739732-chr1:169761259..169763805,3	MCF-7	breast:
3	chr1:169679878..169683283-chr1:169762041..169765464,5	MCF-7	breast:
4	chr1:169738855..169740454-chr1:169761742..169763292,2	K562	blood:
5	chr1:169680417..169682445-chr1:169762164..169765185,3	MCF-7	breast:
6	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

No data

Variant related genes	Relation type
C1orf112	TF binding region
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000188404	Chromatin interaction
ENSG00000117475	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10733054	0.84[EUR][1000 genomes]
rs10737549	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10737550	0.88[ASN][1000 genomes]
rs10737551	0.85[ASN][1000 genomes]
rs10800479	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800480	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10800483	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10800484	0.87[ASN][1000 genomes]
rs10800485	0.96[EUR][1000 genomes]
rs10800486	0.92[EUR][1000 genomes]
rs10919239	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10919245	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919248	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919251	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919257	0.88[ASN][1000 genomes]
rs10919263	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133843	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1883436	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2056980	0.82[EUR][1000 genomes]
rs2056981	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2179396	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2205851	0.84[EUR][1000 genomes]
rs2294322	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294496	0.88[ASN][1000 genomes]
rs2420512	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420514	0.92[EUR][1000 genomes]
rs2491087	0.88[EUR][1000 genomes]
rs2806386	0.86[EUR][1000 genomes]
rs2901179	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3753308	0.93[EUR][1000 genomes]
rs3766132	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766134	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766137	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766142	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766144	0.87[ASN][1000 genomes]
rs3766148	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766151	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3766154	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4376791	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4508080	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4614317	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4615900	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656196	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656197	0.88[ASN][1000 genomes]
rs4656199	0.88[ASN][1000 genomes]
rs4656200	0.88[ASN][1000 genomes]
rs4656721	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656724	0.88[ASN][1000 genomes]
rs4656725	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427217	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6427220	0.92[ASN][1000 genomes]
rs6427224	0.88[ASN][1000 genomes]
rs6427225	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427226	0.82[ASN][1000 genomes]
rs6427227	0.83[ASN][1000 genomes]
rs6427228	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6656965	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664099	0.88[ASN][1000 genomes]
rs6668114	0.93[ASN][1000 genomes]
rs6669794	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6670818	0.93[EUR][1000 genomes]
rs6671752	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6676810	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6680508	0.84[EUR][1000 genomes]
rs6680650	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6680938	0.92[ASN][1000 genomes]
rs6682137	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6682835	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6683056	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684481	0.88[ASN][1000 genomes]
rs6687377	0.86[ASN][1000 genomes]
rs6702969	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs717481	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732185	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7519364	0.88[ASN][1000 genomes]
rs7525259	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526261	0.84[EUR][1000 genomes]
rs7530237	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545011	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287097	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2281039	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs2281039	SCYL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169758600-169763400	Weak transcription	Gastric	stomach
2	chr1:169758800-169763600	Weak transcription	Spleen	Spleen
3	chr1:169760400-169763600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:169762200-169763400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr1:169762600-169763800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:169762600-169765400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:169762800-169763400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr1:169762800-169763400	Flanking Active TSS	Dnd41	blood
9	chr1:169762800-169763600	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr1:169762800-169765200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:169762800-169765400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:169763000-169763400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:169763000-169763400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:169763000-169763400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:169763000-169763400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:169763000-169763400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:169763000-169763400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:169763000-169763400	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr1:169763000-169763400	Enhancers	Placenta	Placenta
20	chr1:169763000-169763400	Flanking Active TSS	A549	lung
21	chr1:169763000-169763400	Flanking Active TSS	NHLF	lung
22	chr1:169763000-169763400	Flanking Active TSS	Osteobl	bone
23	chr1:169763000-169763600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:169763000-169763600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr1:169763000-169763600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:169763000-169763600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr1:169763000-169763600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:169763000-169763600	Flanking Active TSS	Liver	Liver
29	chr1:169763000-169763600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:169763000-169763800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr1:169763000-169764600	Active TSS	Colonic Mucosa	Colon
32	chr1:169763000-169764600	Active TSS	Fetal Brain Female	brain
33	chr1:169763000-169764800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:169763000-169764800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:169763000-169765000	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:169763000-169765000	Active TSS	Fetal Stomach	stomach
37	chr1:169763000-169765200	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr1:169763000-169765200	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:169763000-169765200	Active TSS	K562	blood
40	chr1:169763000-169765600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:169763000-169766400	Active TSS	GM12878-XiMat	blood
42	chr1:169763200-169763400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr1:169763200-169763400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:169763200-169763400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr1:169763200-169763400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:169763200-169763400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr1:169763200-169763400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr1:169763200-169763400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:169763200-169763400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr1:169763200-169763400	Flanking Active TSS	Brain Angular Gyrus	brain

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