Variant report

Variant	rs1412892
Chromosome Location	chr1:170502517-170502518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:170502485-170502877	IMR90	lung:	n/a	chr1:170502850-170502863
2	RAD21	chr1:170500773-170502777	IMR90	lung:	n/a	n/a
3	POLR2A	chr1:170499492-170504188	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:170499618-170503920	IMR90	lung:	n/a	n/a
5	RCOR1	chr1:170502488-170502622	K562	blood:	n/a	n/a
6	POLR2A	chr1:170500668-170503022	GM12878	blood:	n/a	n/a
7	CUX1	chr1:170502460-170502740	K562	blood:	n/a	n/a
8	CEBPB	chr1:170502508-170502821	K562	blood:	n/a	n/a
9	POLR2A	chr1:170500053-170503457	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:170502418-170502656	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr1:170502459-170502900	K562	blood:	n/a	n/a
12	JUND	chr1:170502516-170503028	K562	blood:	n/a	n/a
13	TBL1XR1	chr1:170502262-170502796	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:170502427-170503093	GM12878	blood:	n/a	n/a
15	WRNIP1	chr1:170502342-170503039	GM12878	blood:	n/a	n/a
16	MYC	chr1:170500043-170502806	K562	blood:	n/a	n/a
17	CHD1	chr1:170502450-170502804	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:170500588-170509342	K562	blood:	n/a	n/a
19	MAFK	chr1:170500834-170502695	K562	blood:	n/a	chr1:170501465-170501480 chr1:170502138-170502152
20	POLR2A	chr1:170500523-170502838	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:170501854..170504832-chr1:170526241..170528551,2	MCF-7	breast:
2	chr1:169862177..169865166-chr1:170500254..170502788,2	MCF-7	breast:
3	chr1:169862596..169865250-chr1:170499667..170504019,5	K562	blood:
4	chr1:170499494..170504219-chr1:170507198..170509728,4	K562	blood:
5	chr1:170499494..170507345-chr1:170507805..170517333,18	K562	blood:
6	chr1:170499484..170505100-chr1:170505427..170511134,13	MCF-7	breast:
7	chr1:170500034..170503040-chr1:170504550..170507151,5	K562	blood:
8	chr1:170499846..170504184-chr1:170513564..170517681,4	K562	blood:

No data

Variant related genes	Relation type
GORAB	TF binding region
ENSG00000231407	TF binding region
ENSG00000000457	Chromatin interaction
ENSG00000120370	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10733056	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10753814	0.91[AFR][1000 genomes]
rs10753815	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs10800527	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919425	0.88[AFR][1000 genomes]
rs10919429	1.00[AMR][1000 genomes]
rs12068399	1.00[AMR][1000 genomes]
rs12116909	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1333133	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1333142	1.00[YRI][hapmap]
rs1333150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1333155	0.90[AFR][1000 genomes]
rs1333156	0.90[AFR][1000 genomes]
rs1412893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1412895	0.90[AFR][1000 genomes]
rs1537390	1.00[YRI][hapmap]
rs1537395	0.82[YRI][hapmap]
rs1537397	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs1576979	0.89[AFR][1000 genomes]
rs1576980	0.88[AFR][1000 genomes]
rs16863435	1.00[AMR][1000 genomes]
rs1855221	0.90[AFR][1000 genomes]
rs1928716	1.00[YRI][hapmap]
rs1930632	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2104918	0.87[AFR][1000 genomes]
rs2150029	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2225322	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs2421325	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2901401	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs3980839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4233350	0.82[AFR][1000 genomes]
rs4325194	0.94[AFR][1000 genomes]
rs4402174	0.90[AFR][1000 genomes]
rs4415629	0.94[AFR][1000 genomes]
rs4656769	0.85[AFR][1000 genomes]
rs4656775	0.92[AFR][1000 genomes]
rs4656777	0.92[AFR][1000 genomes]
rs4656779	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs4656783	0.97[AFR][1000 genomes]
rs6427260	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6427261	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6657164	0.90[AFR][1000 genomes]
rs6660575	0.89[AFR][1000 genomes]
rs6664037	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6667304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669308	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6670724	0.88[AFR][1000 genomes]
rs6671312	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676081	0.95[AFR][1000 genomes]
rs6693763	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6699057	0.85[AFR][1000 genomes]
rs6701218	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703801	0.82[AFR][1000 genomes]
rs7523665	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531125	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs7538125	0.90[AFR][1000 genomes]
rs7548443	0.90[AFR][1000 genomes]
rs7553254	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][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	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170499600-170502800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:170499800-170502600	Active TSS	Aorta	Aorta
3	chr1:170500000-170502600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:170500000-170502600	Active TSS	GM12878-XiMat	blood
5	chr1:170500000-170502800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:170500000-170502800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:170500000-170503000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:170500000-170504000	Active TSS	NHLF	lung
9	chr1:170500200-170502600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:170500200-170502600	Active TSS	Brain Germinal Matrix	brain
11	chr1:170500200-170502600	Active TSS	Ovary	ovary
12	chr1:170500200-170502800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:170500200-170502800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:170500200-170502800	Active TSS	Psoas Muscle	Psoas
15	chr1:170500200-170502800	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:170500200-170503000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:170500200-170503000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:170500200-170503000	Active TSS	Right Ventricle	heart
19	chr1:170500200-170503200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:170500200-170503600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:170500400-170502600	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr1:170500400-170502600	Active TSS	NHDF-Ad	bronchial
23	chr1:170500400-170503400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:170500600-170502800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:170501600-170502600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr1:170501600-170503000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:170501800-170502600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:170501800-170502600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr1:170501800-170502600	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr1:170501800-170502600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:170501800-170502600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr1:170501800-170502800	Flanking Active TSS	Liver	Liver
33	chr1:170501800-170502800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr1:170501800-170502800	Flanking Active TSS	HUVEC	blood vessel
35	chr1:170501800-170516000	Weak transcription	Spleen	Spleen
36	chr1:170502000-170502600	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr1:170502000-170502600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr1:170502000-170502600	Weak transcription	Left Ventricle	heart
39	chr1:170502000-170502600	Weak transcription	Lung	lung
40	chr1:170502000-170502600	Weak transcription	Pancreas	Pancrea
41	chr1:170502000-170502600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
42	chr1:170502000-170502600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:170502000-170502600	Active TSS	HepG2	liver
44	chr1:170502000-170502800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:170502000-170502800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:170502000-170502800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:170502000-170502800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:170502000-170502800	Flanking Active TSS	Fetal Heart	heart
49	chr1:170502000-170502800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:170502000-170502800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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