Variant report

Variant	rs62009333
Chromosome Location	chr15:78441574-78441575
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:348)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:348 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:78441252-78442286	GM18951	blood:	n/a	n/a
2	SIN3A	chr15:78441286-78442303	GM12878	blood:	n/a	chr15:78441700-78441711 chr15:78441971-78441984
3	MAX	chr15:78441328-78442012	SK-N-SH	brain:	n/a	chr15:78441858-78441867
4	CUX1	chr15:78441260-78441629	GM12878	blood:	n/a	n/a
5	RUNX3	chr15:78441225-78442305	GM12878	blood:	n/a	chr15:78442235-78442252
6	POLR2A	chr15:78441087-78442224	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr15:78441197-78441918	HCT-116	colon:	n/a	n/a
8	POLR2A	chr15:78440576-78441987	MCF10A-Er-Src	breast:	n/a	n/a
9	TEAD4	chr15:78441199-78441745	K562	blood:	n/a	n/a
10	TAF1	chr15:78441318-78441622	GM12892	blood:	n/a	n/a
11	POLR2A	chr15:78441249-78441936	K562	blood:	n/a	n/a
12	TAF1	chr15:78441329-78441847	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:78441316-78442189	A549	lung:	n/a	n/a
14	RFX5	chr15:78441417-78441737	GM12878	blood:	n/a	n/a
15	MAX	chr15:78441176-78442504	A549	lung:	n/a	chr15:78441858-78441867
16	TAF1	chr15:78441260-78441590	GM12891	blood:	n/a	n/a
17	PAX5	chr15:78441329-78441871	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:78441166-78441583	GM12892	blood:	n/a	n/a
19	POLR2A	chr15:78441048-78442365	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:78441229-78442056	H1-neurons	neurons:	n/a	n/a
21	GABPA	chr15:78441021-78441901	MCF-7	breast:	n/a	chr15:78441695-78441704 chr15:78441693-78441704 chr15:78441693-78441707
22	TAF7	chr15:78441311-78441673	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr15:78441365-78441973	A549	lung:	n/a	n/a
24	HCFC1	chr15:78440450-78442802	Hela-S3	cervix:	n/a	n/a
25	ELF1	chr15:78441172-78441873	SK-N-SH	brain:	n/a	chr15:78441513-78441526
26	POLR2A	chr15:78441119-78441966	PANC-1	pancreas:	n/a	n/a
27	PML	chr15:78440981-78442074	GM12878	blood:	n/a	n/a
28	GABPA	chr15:78441364-78441639	HepG2	liver:	n/a	n/a
29	POLR2A	chr15:78441118-78442029	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:78441342-78442109	HepG2	liver:	n/a	n/a
31	ELF1	chr15:78441179-78441880	K562	blood:	n/a	chr15:78441513-78441526
32	FOS	chr15:78441252-78441655	MCF10A-Er-Src	breast:	n/a	chr15:78441547-78441559
33	FOS	chr15:78441264-78441651	MCF10A-Er-Src	breast:	n/a	chr15:78441547-78441559
34	RCOR1	chr15:78441313-78442165	Hela-S3	cervix:	n/a	n/a
35	GABPA	chr15:78441368-78441838	HepG2	liver:	n/a	chr15:78441695-78441704 chr15:78441693-78441704 chr15:78441693-78441707
36	POLR2A	chr15:78441170-78441980	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr15:78441252-78442231	K562	blood:	n/a	n/a
38	PML	chr15:78441277-78441902	K562	blood:	n/a	n/a
39	GABPA	chr15:78441057-78441812	SK-N-SH	brain:	n/a	chr15:78441695-78441704 chr15:78441693-78441704 chr15:78441693-78441707
40	STAT5A	chr15:78441176-78441615	GM12878	blood:	n/a	chr15:78441486-78441506
41	POLR2A	chr15:78441312-78441607	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr15:78441323-78442145	GM12878	blood:	n/a	chr15:78441858-78441867
43	EGR1	chr15:78441568-78442044	ECC-1	luminal epithelium:	n/a	chr15:78441694-78441703 chr15:78442013-78442023 chr15:78441844-78441857 chr15:78442013-78442026 chr15:78441928-78441938
44	SMC3	chr15:78441370-78441753	Hela-S3	cervix:	n/a	n/a
45	ELF1	chr15:78441115-78441804	HCT-116	colon:	n/a	chr15:78441513-78441526
46	NFIC	chr15:78441343-78441789	SK-N-SH	brain:	n/a	n/a
47	NFYA	chr15:78441383-78441792	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr15:78441250-78442659	Raji	blood:	n/a	n/a
49	RELA	chr15:78441228-78442304	GM15510	blood:	n/a	n/a
50	MAX	chr15:78441340-78442402	MCF-7	breast:	n/a	chr15:78441858-78441867

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:78441560-78441610	SKMC	muscle:	n/a
2	chr15:78441560-78441610	AG04450	lung:	fetal
3	chr15:78441560-78441610	HCF	heart:	n/a
4	chr15:78441560-78441610	BE2_C	brain:	n/a
5	chr15:78441560-78441610	AoSMC	blood vessel:	n/a
6	chr15:78441560-78441610	LNCaP	prostate:	n/a
7	chr15:78441560-78441610	HPAEpiC	pulmonary alveolar:	n/a
8	chr15:78441560-78441610	GM12892	blood:	n/a
9	chr15:78441560-78441610	HCT-116	colon:	n/a
10	chr15:78441560-78441610	SK-N-MC	brain:	n/a
11	chr15:78441560-78441610	NH-A	brain:	n/a
12	chr15:78441560-78441610	GM19239	blood:	n/a
13	chr15:78441560-78441610	HL-60	blood:	n/a
14	chr15:78441560-78441610	PANC-1	pancreas:	n/a
15	chr15:78441560-78441610	NHBE	bronchial:	n/a
16	chr15:78441560-78441610	Caco-2	colon:	n/a
17	chr15:78441560-78441610	HCPEpiC	choroid plexus:	n/a
18	chr15:78441560-78441610	HIPEpiC	eye:	n/a
19	chr15:78441560-78441610	NHDF-neo	bronchial:	n/a
20	chr15:78441560-78441610	SK-N-SH_RA	brain:	n/a
21	chr15:78441560-78441610	ProgFib	skin:	n/a
22	chr15:78441560-78441610	ovcar-3	ovarian:	n/a
23	chr15:78441560-78441610	AG09309	skin:	n/a
24	chr15:78441560-78441610	HRCEpiC	kidney:	n/a
25	chr15:78441560-78441610	GM06990	blood:	n/a
26	chr15:78441560-78441610	IMR90	lung:	fetal
27	chr15:78441560-78441610	AG10803	skin:	n/a
28	chr15:78441560-78441610	K562	blood:	n/a
29	chr15:78441560-78441610	NB4	blood:	n/a
30	chr15:78441560-78441610	HUVEC	blood vessel:	n/a
31	chr15:78441560-78441610	RPTEC	kidney:	n/a
32	chr15:78441560-78441610	HepG2	liver:	n/a
33	chr15:78441560-78441610	Hela-S3	cervix:	n/a
34	chr15:78441560-78441610	HNPCEpiC	eye:	n/a
35	chr15:78441560-78441610	HRE	kidney:	n/a
36	chr15:78441560-78441610	MCF-7	breast:	n/a
37	chr15:78441560-78441610	PrEC	prostate:	n/a
38	chr15:78441560-78441610	H1-hESC	embryonic stem cell:	embryo
39	chr15:78441560-78441610	A549	lung:	n/a
40	chr15:78441560-78441610	SAEC	small airway:	n/a
41	chr15:78441560-78441610	AG09319	gingival:	n/a
42	chr15:78441560-78441610	MCF10A-Er-Src	breast:	n/a
43	chr15:78441560-78441610	Hepatocyte	liver:	n/a
44	chr15:78441560-78441610	U87	brain:	n/a
45	chr15:78441560-78441610	HMEC	breast:	n/a
46	chr15:78441560-78441610	GM12891	blood:	n/a
47	chr15:78441560-78441610	Jurkat	blood:	n/a
48	chr15:78441560-78441610	HCM	heart:	n/a
49	chr15:78441560-78441610	HAEpiC	amniotic membrane:	n/a
50	chr15:78441560-78441610	SK-N-SH	brain:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78441071..78441786-chr3:23959166..23959779,2	Hela-S3	cervix:
2	chr15:78421103..78425437-chr15:78438436..78443517,9	MCF-7	breast:
3	chr15:78440397..78443186-chr15:78499689..78503898,3	MCF-7	breast:
4	chr15:78439170..78443635-chr15:78452310..78455814,4	K562	blood:
5	chr15:78441557..78443629-chr15:78465322..78467706,2	MCF-7	breast:
6	chr15:78440356..78444633-chr15:78445807..78449726,8	K562	blood:
7	chr15:78440859..78443747-chr15:78450376..78455479,5	K562	blood:
8	chr15:78422180..78427678-chr15:78438636..78444300,13	MCF-7	breast:
9	chr15:78422233..78425731-chr15:78438987..78443227,7	K562	blood:
10	chr15:78433535..78435923-chr15:78440184..78443056,4	K562	blood:
11	chr14:45430537..45431179-chr15:78441265..78442106,2	Hela-S3	cervix:
12	chr15:78422015..78425228-chr15:78439030..78443289,7	K562	blood:
13	chr15:78440947..78441580-chr16:74734168..74734671,2	Hela-S3	cervix:
14	chr15:78440410..78443288-chr15:78589688..78592209,3	K562	blood:

No data

Variant related genes	Relation type
IDH3A	TF binding region
IDH3A	CpG island
ENSG00000174748	Chromatin interaction
ENSG00000103740	Chromatin interaction
ENSG00000140395	Chromatin interaction
ENSG00000260988	Chromatin interaction
ENSG00000136425	Chromatin interaction
ENSG00000179454	Chromatin interaction
ENSG00000166411	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11854120	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856106	0.94[ASN][1000 genomes]
rs17479031	1.00[ASN][1000 genomes]
rs17479135	1.00[ASN][1000 genomes]
rs17850483	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17850484	1.00[ASN][1000 genomes]
rs3825847	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4570804	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57867560	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009331	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62009334	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009335	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009336	0.89[EUR][1000 genomes]
rs62009337	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009339	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009340	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009341	0.89[EUR][1000 genomes]
rs62009342	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009343	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165154	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv3340405	chr15:78440522-78443070	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78440200-78442400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:78440600-78441800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:78440600-78442000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:78440600-78442200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr15:78440600-78442400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:78440600-78442400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:78440600-78442400	Active TSS	Muscle Satellite Cultured Cells	--
8	chr15:78440600-78442400	Active TSS	Colonic Mucosa	Colon
9	chr15:78440600-78442400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr15:78440600-78442400	Active TSS	Fetal Brain Male	brain
11	chr15:78440600-78442600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr15:78440600-78442600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:78440800-78441600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:78440800-78441600	Weak transcription	Esophagus	oesophagus
15	chr15:78440800-78441600	Weak transcription	Gastric	stomach
16	chr15:78440800-78441800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:78440800-78442000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr15:78440800-78442200	Active TSS	Brain Hippocampus Middle	brain
19	chr15:78440800-78442200	Active TSS	Colon Smooth Muscle	Colon
20	chr15:78440800-78442400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr15:78440800-78442400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:78440800-78442400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:78440800-78442400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:78440800-78442600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr15:78440800-78442800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:78440800-78442800	Active TSS	Brain Germinal Matrix	brain
27	chr15:78440800-78442800	Active TSS	HSMMtube	muscle
28	chr15:78440800-78443400	Active TSS	Right Atrium	heart
29	chr15:78441000-78441800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:78441000-78441800	Weak transcription	Spleen	Spleen
31	chr15:78441000-78441800	Active TSS	HepG2	liver
32	chr15:78441000-78442000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:78441000-78442000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:78441000-78442200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr15:78441000-78442200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr15:78441000-78442200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:78441000-78442200	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr15:78441000-78442200	Active TSS	Primary T cells from cord blood	blood
39	chr15:78441000-78442200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:78441000-78442200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:78441000-78442200	Active TSS	Brain Angular Gyrus	brain
42	chr15:78441000-78442200	Active TSS	Brain Cingulate Gyrus	brain
43	chr15:78441000-78442200	Active TSS	HMEC	breast
44	chr15:78441000-78442200	Active TSS	K562	blood
45	chr15:78441000-78442400	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr15:78441000-78442400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:78441000-78442400	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr15:78441000-78442400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:78441000-78442400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:78441000-78442400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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