Variant report

Variant	rs7553254
Chromosome Location	chr1:170500870-170500871
allele	C/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	PBX3	chr1:170500675-170501855	SK-N-SH	brain:	n/a	chr1:170501260-170501269
2	POLR2A	chr1:170500639-170502010	H1-hESC	embryonic stem cell:	n/a	n/a
3	RCOR1	chr1:170500794-170501759	GM12878	blood:	n/a	n/a
4	HCFC1	chr1:170500562-170502400	Hela-S3	cervix:	n/a	n/a
5	SP1	chr1:170500628-170501797	A549	lung:	n/a	chr1:170501503-170501513 chr1:170501474-170501483 chr1:170501469-170501483 chr1:170500797-170500807
6	MAX	chr1:170500718-170501813	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:170500743-170501810	HUVEC	blood vessel:	n/a	n/a
8	IRF1	chr1:170500811-170501759	K562	blood:	n/a	chr1:170501261-170501270 chr1:170501472-170501486 chr1:170501502-170501516
9	TBP	chr1:170500694-170502321	GM12878	blood:	n/a	n/a
10	RUNX3	chr1:170500677-170501771	GM12878	blood:	n/a	n/a
11	USF1	chr1:170500760-170501372	A549	lung:	n/a	n/a
12	SIN3AK20	chr1:170500799-170501275	A549	lung:	n/a	n/a
13	ELF1	chr1:170500798-170501836	MCF-7	breast:	n/a	chr1:170501267-170501279 chr1:170501216-170501228
14	TAF1	chr1:170500670-170501674	MCF-7	breast:	n/a	n/a
15	ARID3A	chr1:170500705-170501967	HepG2	liver:	n/a	n/a
16	TBP	chr1:170500698-170501832	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr1:170500812-170501717	K562	blood:	n/a	n/a
18	BCLAF1	chr1:170500647-170501787	GM12878	blood:	n/a	chr1:170501266-170501279 chr1:170501538-170501546
19	BCL3	chr1:170500587-170501673	A549	lung:	n/a	chr1:170501266-170501279 chr1:170501538-170501546
20	GABPA	chr1:170500799-170501902	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr1:170500674-170501853	ECC-1	luminal epithelium:	n/a	n/a
22	YY1	chr1:170500801-170501802	HCT-116	colon:	n/a	chr1:170500939-170500950
23	SPI1	chr1:170500585-170501926	HL-60	blood:	n/a	n/a
24	EP300	chr1:170500603-170502035	K562	blood:	n/a	n/a
25	POU2F2	chr1:170500751-170501809	GM12891	blood:	n/a	n/a
26	CHD2	chr1:170500761-170501825	Hela-S3	cervix:	n/a	n/a
27	ZEB1	chr1:170500850-170501004	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:170500687-170501865	Hela-S3	cervix:	n/a	n/a
29	ZNF143	chr1:170500749-170501836	K562	blood:	n/a	chr1:170501189-170501208
30	POLR2A	chr1:170500655-170501932	K562	blood:	n/a	n/a
31	MAX	chr1:170500676-170501534	ECC-1	luminal epithelium:	n/a	n/a
32	ZNF263	chr1:170500785-170502014	HEK293-T-REx	kidney:	n/a	n/a
33	ZNF143	chr1:170500731-170501769	GM12878	blood:	n/a	chr1:170501189-170501208
34	SMC3	chr1:170500715-170501732	GM12878	blood:	n/a	n/a
35	FOXM1	chr1:170500663-170501581	GM12878	blood:	n/a	n/a
36	CHD2	chr1:170500867-170501742	K562	blood:	n/a	n/a
37	MYC	chr1:170500788-170501948	NB4	blood:	n/a	n/a
38	SMARCB1	chr1:170500749-170501965	Hela-S3	cervix:	n/a	n/a
39	IRF4	chr1:170500829-170501454	GM12878	blood:	n/a	n/a
40	RAD21	chr1:170500773-170502777	IMR90	lung:	n/a	n/a
41	ATF3	chr1:170500751-170501327	A549	lung:	n/a	n/a
42	TAF1	chr1:170500538-170501804	A549	lung:	n/a	n/a
43	POLR2A	chr1:170500744-170501889	NB4	blood:	n/a	n/a
44	MAZ	chr1:170500770-170501833	K562	blood:	n/a	n/a
45	YY1	chr1:170500824-170501722	SK-N-SH_RA	brain:	n/a	chr1:170500939-170500950
46	MAFK	chr1:170500831-170501890	Hela-S3	cervix:	n/a	chr1:170501465-170501480
47	POLR2A	chr1:170500407-170502342	GM19099	blood:	n/a	n/a
48	POLR2A	chr1:170499492-170504188	GM12878	blood:	n/a	n/a
49	PML	chr1:170500761-170501999	K562	blood:	n/a	n/a
50	POLR2A	chr1:170500840-170501430	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:170499982..170502014-chr3:62799572..62801827,2	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	chr1:170500119..170501652-chr1:170512143..170514479,2	MCF-7	breast:
9	chr1:170499846..170504184-chr1:170513564..170517681,4	K562	blood:

Variant related genes	Relation type
GORAB	TF binding region
ENSG00000000457	Chromatin interaction
ENSG00000252449	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];0.90[AFR][1000 genomes]
rs10753814	0.93[AFR][1000 genomes]
rs10753815	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs10800527	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919425	0.90[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1333155	0.90[AFR][1000 genomes]
rs1333156	0.90[AFR][1000 genomes]
rs1412892	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1412893	0.98[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];0.93[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];0.91[AFR][1000 genomes]
rs2225322	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs2421325	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2901401	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3980839	0.98[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	0.96[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];0.90[AFR][1000 genomes]
rs4656783	0.95[AFR][1000 genomes]
rs6427260	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6427261	1.00[YRI][hapmap];0.98[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6667304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669308	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6670724	0.88[AFR][1000 genomes]
rs6671312	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676081	0.93[AFR][1000 genomes]
rs6693763	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6699057	0.85[AFR][1000 genomes]
rs6701218	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703801	0.82[AFR][1000 genomes]
rs7523665	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531125	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs7538125	0.90[AFR][1000 genomes]
rs7548443	0.92[AFR][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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170499600-170501800	Active TSS	Brain Anterior Caudate	brain
2	chr1:170499600-170502800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:170499800-170502000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:170499800-170502600	Active TSS	Aorta	Aorta
5	chr1:170500000-170501000	Active TSS	Right Atrium	heart
6	chr1:170500000-170501800	Active TSS	Adipose Nuclei	Adipose
7	chr1:170500000-170501800	Active TSS	Brain Angular Gyrus	brain
8	chr1:170500000-170501800	Active TSS	Brain Cingulate Gyrus	brain
9	chr1:170500000-170501800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr1:170500000-170502000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:170500000-170502000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:170500000-170502000	Active TSS	Brain Hippocampus Middle	brain
13	chr1:170500000-170502000	Active TSS	Duodenum Mucosa	Duodenum
14	chr1:170500000-170502000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:170500000-170502000	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:170500000-170502200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:170500000-170502200	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr1:170500000-170502200	Active TSS	Muscle Satellite Cultured Cells	--
19	chr1:170500000-170502200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:170500000-170502200	Active TSS	Fetal Brain Male	brain
21	chr1:170500000-170502200	Active TSS	Fetal Muscle Leg	muscle
22	chr1:170500000-170502200	Active TSS	NHEK	skin
23	chr1:170500000-170502400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr1:170500000-170502400	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr1:170500000-170502400	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr1:170500000-170502400	Active TSS	Fetal Intestine Large	intestine
27	chr1:170500000-170502400	Active TSS	HMEC	breast
28	chr1:170500000-170502400	Active TSS	K562	blood
29	chr1:170500000-170502400	Active TSS	NH-A	brain
30	chr1:170500000-170502600	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:170500000-170502600	Active TSS	GM12878-XiMat	blood
32	chr1:170500000-170502800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:170500000-170502800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:170500000-170503000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:170500000-170504000	Active TSS	NHLF	lung
36	chr1:170500200-170501000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:170500200-170501600	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:170500200-170501800	Active TSS	Primary T cells from cord blood	blood
39	chr1:170500200-170501800	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:170500200-170501800	Active TSS	Liver	Liver
41	chr1:170500200-170501800	Active TSS	Colon Smooth Muscle	Colon
42	chr1:170500200-170501800	Active TSS	Fetal Brain Female	brain
43	chr1:170500200-170501800	Active TSS	Spleen	Spleen
44	chr1:170500200-170501800	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr1:170500200-170502000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:170500200-170502000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:170500200-170502000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:170500200-170502000	Active TSS	Brain Substantia Nigra	brain
49	chr1:170500200-170502000	Active TSS	Esophagus	oesophagus
50	chr1:170500200-170502000	Active TSS	Left Ventricle	heart

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