Variant report

Variant	rs9962380
Chromosome Location	chr18:43678706-43678707
allele	C/T
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	GABPA	chr18:43677915-43678808	A549	lung:	n/a	chr18:43678339-43678348 chr18:43678070-43678084
2	USF1	chr18:43677990-43679036	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr18:43677380-43678822	IMR90	lung:	n/a	chr18:43678508-43678517 chr18:43678295-43678304 chr18:43678510-43678519
4	MAX	chr18:43677750-43679086	A549	lung:	n/a	chr18:43678507-43678520 chr18:43678508-43678519 chr18:43678509-43678519 chr18:43678509-43678519 chr18:43678507-43678522 chr18:43678508-43678519 chr18:43678346-43678356 chr18:43678508-43678518 chr18:43678509-43678518 chr18:43678508-43678517
5	POLR2A	chr18:43677437-43679245	Raji	blood:	n/a	n/a
6	MAX	chr18:43677734-43678955	NB4	blood:	n/a	chr18:43678507-43678520 chr18:43678508-43678519 chr18:43678509-43678519 chr18:43678509-43678519 chr18:43678507-43678522 chr18:43678508-43678519 chr18:43678346-43678356 chr18:43678508-43678518 chr18:43678509-43678518 chr18:43678508-43678517
7	FOXM1	chr18:43678347-43678714	GM12878	blood:	n/a	n/a
8	POLR2A	chr18:43677785-43678811	NB4	blood:	n/a	n/a
9	POLR2A	chr18:43677770-43678759	HCT-116	colon:	n/a	n/a
10	POLR2A	chr18:43678474-43678730	GM12878	blood:	n/a	n/a
11	MXI1	chr18:43677507-43678824	HepG2	liver:	n/a	chr18:43678508-43678517 chr18:43678295-43678304 chr18:43678510-43678519
12	MYC	chr18:43677828-43678760	K562	blood:	n/a	chr18:43678507-43678520 chr18:43678508-43678519 chr18:43678509-43678519 chr18:43678509-43678519 chr18:43678507-43678522 chr18:43678508-43678519 chr18:43678346-43678356 chr18:43678508-43678518 chr18:43678509-43678518 chr18:43678508-43678517
13	POLR2A	chr18:43677724-43679045	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr18:43678462-43678740	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAFK	chr18:43678405-43678740	K562	blood:	n/a	n/a
16	TAF1	chr18:43677695-43678714	GM12878	blood:	n/a	n/a
17	POLR2A	chr18:43678380-43678772	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr18:43677820-43678880	U87	brain:	n/a	n/a
19	CHD2	chr18:43677592-43678735	GM12878	blood:	n/a	n/a
20	POLR2A	chr18:43677386-43678809	GM12892	blood:	n/a	n/a
21	MAZ	chr18:43677595-43678732	K562	blood:	n/a	chr18:43678507-43678520 chr18:43678508-43678519 chr18:43678509-43678519 chr18:43678509-43678519 chr18:43678507-43678522 chr18:43678508-43678519 chr18:43678346-43678356 chr18:43678508-43678518 chr18:43678509-43678518 chr18:43678508-43678517
22	TAF1	chr18:43677398-43678763	ECC-1	luminal epithelium:	n/a	n/a
23	GABPA	chr18:43677779-43679053	MCF-7	breast:	n/a	chr18:43678339-43678348 chr18:43678070-43678084
24	YY1	chr18:43677428-43678756	H1-hESC	embryonic stem cell:	n/a	chr18:43678342-43678353 chr18:43678339-43678348 chr18:43678023-43678031 chr18:43678340-43678354 chr18:43678022-43678032 chr18:43678015-43678034 chr18:43678339-43678353 chr18:43678345-43678354 chr18:43678342-43678351 chr18:43678021-43678029
25	GABPA	chr18:43677742-43678788	K562	blood:	n/a	chr18:43678339-43678348 chr18:43678070-43678084
26	POLR2A	chr18:43678405-43678733	A549	lung:	n/a	n/a
27	CHD2	chr18:43677782-43679053	Hela-S3	cervix:	n/a	n/a
28	RCOR1	chr18:43677846-43678852	K562	blood:	n/a	n/a
29	MAX	chr18:43677625-43678880	K562	blood:	n/a	chr18:43678507-43678520 chr18:43678508-43678519 chr18:43678509-43678519 chr18:43678509-43678519 chr18:43678507-43678522 chr18:43678508-43678519 chr18:43678346-43678356 chr18:43678508-43678518 chr18:43678509-43678518 chr18:43678508-43678517
30	USF2	chr18:43678136-43678739	Hela-S3	cervix:	n/a	n/a
31	USF1	chr18:43678119-43678926	SK-N-SH_RA	brain:	n/a	n/a
32	POLR2A	chr18:43677435-43678880	GM19193	blood:	n/a	n/a
33	USF1	chr18:43677980-43678826	ECC-1	luminal epithelium:	n/a	n/a
34	SIN3AK20	chr18:43677726-43678724	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr18:43677378-43678842	GM18951	blood:	n/a	n/a
36	POLR2A	chr18:43677506-43678821	GM12892	blood:	n/a	n/a
37	MAX	chr18:43677638-43678839	HCT-116	colon:	n/a	chr18:43678507-43678520 chr18:43678508-43678519 chr18:43678509-43678519 chr18:43678509-43678519 chr18:43678507-43678522 chr18:43678508-43678519 chr18:43678346-43678356 chr18:43678508-43678518 chr18:43678509-43678518 chr18:43678508-43678517
38	POLR2A	chr18:43677987-43678812	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr18:43676770-43678829	GM12878	blood:	n/a	n/a
40	POLR2A	chr18:43677735-43678841	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr18:43677692-43679148	MCF10A-Er-Src	breast:	n/a	n/a
42	MYC	chr18:43678008-43678767	K562	blood:	n/a	chr18:43678507-43678520 chr18:43678508-43678519 chr18:43678509-43678519 chr18:43678509-43678519 chr18:43678507-43678522 chr18:43678508-43678519 chr18:43678346-43678356 chr18:43678508-43678518 chr18:43678509-43678518 chr18:43678508-43678517
43	POLR2A	chr18:43677504-43678830	Hela-S3	cervix:	n/a	n/a
44	EGR1	chr18:43677700-43678733	HCT-116	colon:	n/a	chr18:43678340-43678350 chr18:43678340-43678353 chr18:43678344-43678354 chr18:43678339-43678354 chr18:43678338-43678348 chr18:43678340-43678353 chr18:43678341-43678350 chr18:43678340-43678353
45	GABPA	chr18:43677937-43678746	MCF-7	breast:	n/a	chr18:43678339-43678348 chr18:43678070-43678084
46	MXI1	chr18:43677065-43678770	Hela-S3	cervix:	n/a	chr18:43678508-43678517 chr18:43678295-43678304 chr18:43677214-43677229 chr18:43678510-43678519
47	SIN3A	chr18:43677380-43678733	GM12878	blood:	n/a	chr18:43678508-43678517
48	TAF1	chr18:43678414-43678706	K562	blood:	n/a	n/a
49	GABPA	chr18:43677968-43678787	HL-60	blood:	n/a	chr18:43678339-43678348 chr18:43678070-43678084
50	POLR2A	chr18:43677811-43678748	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:43676160..43680812-chr18:43682051..43685941,8	K562	blood:
2	chr18:43677240..43681670-chr18:43684014..43685946,4	K562	blood:
3	chr18:43676858..43680433-chr18:43682158..43685518,5	MCF-7	breast:
4	chr18:43669948..43672641-chr18:43676747..43679041,2	K562	blood:
5	chr18:43678466..43679007-chr19:1269155..1269840,2	HCT-116	colon:
6	chr18:43678336..43678927-chr9:140135276..140135883,2	HCT-116	colon:
7	chr18:43671592..43673196-chr18:43677862..43679768,2	MCF-7	breast:
8	chr18:43671600..43674875-chr18:43675841..43678916,7	K562	blood:

Variant related genes	Relation type
ATP5A1	TF binding region
ENSG00000152234	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000152240	Chromatin interaction
ENSG00000099622	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11082509	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11082510	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11659357	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11659478	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11659795	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11661945	0.91[EUR][1000 genomes]
rs11664764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11872954	0.92[EUR][1000 genomes]
rs11872985	0.92[EUR][1000 genomes]
rs11874712	0.93[EUR][1000 genomes]
rs12954944	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381709	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800637	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800639	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800640	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298787	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457840	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28504655	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532950	0.85[EUR][1000 genomes]
rs28699609	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28757346	0.84[EUR][1000 genomes]
rs34907121	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35507656	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3765636	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56075249	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56181324	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62096500	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71364522	0.85[EUR][1000 genomes]
rs7230064	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7235373	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7244921	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085444	0.89[EUR][1000 genomes]
rs8085743	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8088881	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8089150	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091452	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8092674	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8093880	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8094902	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095031	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097521	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9304326	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304327	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304328	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9304330	0.82[EUR][1000 genomes]
rs9783884	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9783887	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9783888	0.90[EUR][1000 genomes]
rs9944637	0.90[EUR][1000 genomes]
rs9945606	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9945751	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9947908	0.89[EUR][1000 genomes]
rs9954278	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9961065	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9962458	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv962965	chr18:43678008-43706302	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43674600-43678800	Active TSS	Right Atrium	heart
2	chr18:43676000-43678800	Active TSS	Psoas Muscle	Psoas
3	chr18:43676000-43679000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr18:43676400-43678800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:43676400-43678800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr18:43676400-43678800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr18:43676400-43678800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr18:43676400-43678800	Active TSS	K562	blood
9	chr18:43676400-43679000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr18:43676400-43679000	Active TSS	HSMMtube	muscle
11	chr18:43676400-43679200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr18:43676600-43678800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr18:43676600-43678800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr18:43676600-43678800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr18:43676600-43678800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr18:43676600-43678800	Active TSS	Lung	lung
17	chr18:43676600-43678800	Active TSS	Ovary	ovary
18	chr18:43676600-43679200	Active TSS	Fetal Kidney	kidney
19	chr18:43676800-43678800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr18:43676800-43678800	Active TSS	Gastric	stomach
21	chr18:43676800-43679000	Active TSS	Brain Germinal Matrix	brain
22	chr18:43676800-43679000	Active TSS	Brain Substantia Nigra	brain
23	chr18:43676800-43679000	Active TSS	Right Ventricle	heart
24	chr18:43676800-43679000	Active TSS	Stomach Smooth Muscle	stomach
25	chr18:43677000-43678800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr18:43677000-43679000	Active TSS	Fetal Brain Female	brain
27	chr18:43677200-43678800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr18:43677200-43678800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr18:43677200-43678800	Active TSS	Brain Cingulate Gyrus	brain
30	chr18:43678000-43678800	Active TSS	HepG2	liver
31	chr18:43678000-43679000	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr18:43678200-43678800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:43678400-43678800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr18:43678400-43678800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr18:43678400-43678800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr18:43678400-43678800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:43678400-43678800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr18:43678400-43678800	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr18:43678400-43678800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr18:43678400-43678800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr18:43678400-43678800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr18:43678400-43678800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr18:43678400-43678800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr18:43678400-43678800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr18:43678400-43678800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr18:43678400-43678800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr18:43678400-43678800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:43678400-43678800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:43678400-43678800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr18:43678400-43678800	Flanking Active TSS	Adipose Nuclei	Adipose

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