Variant report

Variant	rs754641
Chromosome Location	chr15:59981590-59981591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:408)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:408 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr15:59980620-59981704	A549	lung:	n/a	n/a
2	POLR2A	chr15:59980530-59981886	GM12878	blood:	n/a	n/a
3	RCOR1	chr15:59981304-59981907	K562	blood:	n/a	n/a
4	EP300	chr15:59981488-59981833	GM12878	blood:	n/a	n/a
5	MXI1	chr15:59981146-59981828	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr15:59981436-59981751	MCF-7	breast:	n/a	n/a
7	MAX	chr15:59981114-59981807	HepG2	liver:	n/a	n/a
8	MAX	chr15:59980829-59982051	ECC-1	luminal epithelium:	n/a	n/a
9	ELF1	chr15:59980700-59981846	HepG2	liver:	n/a	n/a
10	RFX5	chr15:59981476-59981913	GM12878	blood:	n/a	n/a
11	FOXA2	chr15:59980792-59981868	A549	lung:	n/a	n/a
12	MAZ	chr15:59980723-59982053	K562	blood:	n/a	n/a
13	GABPA	chr15:59981198-59981746	GM12878	blood:	n/a	n/a
14	JUND	chr15:59980647-59982288	K562	blood:	n/a	n/a
15	MAX	chr15:59980606-59982493	A549	lung:	n/a	n/a
16	POLR2A	chr15:59981154-59981843	A549	lung:	n/a	n/a
17	FOXM1	chr15:59981091-59981960	GM12878	blood:	n/a	n/a
18	BACH1	chr15:59981531-59981846	H1-hESC	embryonic stem cell:	n/a	n/a
19	GABPA	chr15:59981088-59981763	HepG2	liver:	n/a	n/a
20	YY1	chr15:59981307-59981891	SK-N-SH_RA	brain:	n/a	n/a
21	POLR2A	chr15:59981082-59982094	U87	brain:	n/a	n/a
22	CREB1	chr15:59981404-59981887	ECC-1	luminal epithelium:	n/a	n/a
23	SIX5	chr15:59981327-59981617	GM12878	blood:	n/a	n/a
24	CEBPB	chr15:59981414-59982275	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr15:59981045-59981875	SK-N-SH	brain:	n/a	n/a
26	PML	chr15:59980766-59982176	K562	blood:	n/a	n/a
27	CREB1	chr15:59981357-59982051	A549	lung:	n/a	n/a
28	MAZ	chr15:59980806-59982030	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:59980721-59981872	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:59980050-59982314	NB4	blood:	n/a	n/a
31	POLR2A	chr15:59981141-59981884	HepG2	liver:	n/a	n/a
32	BRCA1	chr15:59980439-59982136	Hela-S3	cervix:	n/a	n/a
33	FOXA1	chr15:59981392-59981846	T-47D	breast:	n/a	n/a
34	POLR2A	chr15:59981150-59981857	GM12892	blood:	n/a	n/a
35	EP300	chr15:59981566-59982010	GM12878	blood:	n/a	n/a
36	UBTF	chr15:59980888-59981917	K562	blood:	n/a	n/a
37	MAZ	chr15:59980921-59981911	HepG2	liver:	n/a	n/a
38	EGR1	chr15:59981449-59981812	GM12878	blood:	n/a	chr15:59981601-59981615 chr15:59981584-59981598
39	YY1	chr15:59981365-59981912	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr15:59981146-59981871	HepG2	liver:	n/a	n/a
41	CEBPD	chr15:59981393-59981881	K562	blood:	n/a	n/a
42	MAX	chr15:59980942-59982013	HepG2	liver:	n/a	n/a
43	FOXP2	chr15:59981292-59981857	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr15:59980641-59982236	K562	blood:	n/a	n/a
45	EGR1	chr15:59981310-59981918	K562	blood:	n/a	chr15:59981601-59981615 chr15:59981584-59981598
46	GTF2F1	chr15:59981357-59981876	K562	blood:	n/a	n/a
47	TAF1	chr15:59981165-59981777	HepG2	liver:	n/a	n/a
48	RCOR1	chr15:59981506-59981870	GM12878	blood:	n/a	n/a
49	TAF1	chr15:59981168-59981816	HepG2	liver:	n/a	n/a
50	MXI1	chr15:59980247-59981945	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:59981549-59981599	Hela-S3	cervix:	n/a
2	chr15:59981549-59981599	PrEC	prostate:	n/a
3	chr15:59981549-59981599	GM06990	blood:	n/a
4	chr15:59981549-59981599	PFSK-1	brain:	n/a
5	chr15:59981549-59981599	HCF	heart:	n/a
6	chr15:59981549-59981599	GM12878	blood:	n/a
7	chr15:59981549-59981599	HIPEpiC	eye:	n/a
8	chr15:59981549-59981599	T-47D	breast:	n/a
9	chr15:59981549-59981599	AG09309	skin:	n/a
10	chr15:59981549-59981599	NHBE	bronchial:	n/a
11	chr15:59981549-59981599	AG04449	skin:	fetal
12	chr15:59981549-59981599	SAEC	small airway:	n/a
13	chr15:59981549-59981599	HRPEpiC	eye:	n/a
14	chr15:59981549-59981599	AG09319	gingival:	n/a
15	chr15:59981549-59981599	HCT-116	colon:	n/a
16	chr15:59981549-59981599	LNCaP	prostate:	n/a
17	chr15:59981549-59981599	IMR90	lung:	fetal
18	chr15:59981549-59981599	NB4	blood:	n/a
19	chr15:59981549-59981599	SK-N-SH_RA	brain:	n/a
20	chr15:59981549-59981599	K562	blood:	n/a
21	chr15:59981549-59981599	SKMC	muscle:	n/a
22	chr15:59981549-59981599	HEK293	kidney:	embryo
23	chr15:59981549-59981599	SK-N-MC	brain:	n/a
24	chr15:59981549-59981599	ovcar-3	ovarian:	n/a
25	chr15:59981549-59981599	AG04450	lung:	fetal
26	chr15:59981549-59981599	HCM	heart:	n/a
27	chr15:59981549-59981599	HCPEpiC	choroid plexus:	n/a
28	chr15:59981549-59981599	ProgFib	skin:	n/a
29	chr15:59981549-59981599	HAEpiC	amniotic membrane:	n/a
30	chr15:59981549-59981599	Hepatocyte	liver:	n/a
31	chr15:59981549-59981599	NH-A	brain:	n/a
32	chr15:59981549-59981599	HRCEpiC	kidney:	n/a
33	chr15:59981549-59981599	HPAEpiC	pulmonary alveolar:	n/a
34	chr15:59981549-59981599	HRE	kidney:	n/a
35	chr15:59981549-59981599	HMEC	breast:	n/a
36	chr15:59981549-59981599	BJ	skin:	n/a
37	chr15:59981549-59981599	NT2-D1	testis:	n/a
38	chr15:59981549-59981599	MCF-7	breast:	n/a
39	chr15:59981549-59981599	H1-hESC	embryonic stem cell:	embryo
40	chr15:59981549-59981599	BE2_C	brain:	n/a
41	chr15:59981549-59981599	PANC-1	pancreas:	n/a
42	chr15:59981549-59981599	HUVEC	blood vessel:	n/a
43	chr15:59981549-59981599	U87	brain:	n/a
44	chr15:59981549-59981599	Caco-2	colon:	n/a
45	chr15:59981549-59981599	NHDF-neo	bronchial:	n/a
46	chr15:59981549-59981599	HEEpiC	esophagus:	n/a
47	chr15:59981549-59981599	GM12892	blood:	n/a
48	chr15:59981549-59981599	MCF10A-Er-Src	breast:	n/a
49	chr15:59981549-59981599	GM19239	blood:	n/a
50	chr15:59981549-59981599	Jurkat	blood:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59981055..59982632-chr15:60666693..60668743,2	MCF-7	breast:
2	chr15:59980654..59981595-chr17:57915006..57915812,2	Hela-S3	cervix:
3	chr15:59981089..59981683-chr5:154237614..154238529,2	Hela-S3	cervix:
4	chr15:59979548..59984505-chr15:60688391..60691990,7	K562	blood:
5	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:
6	chr11:18417073..18418064-chr15:59981374..59982004,2	Hela-S3	cervix:
7	chr15:59979537..59982042-chr15:60770595..60772312,3	K562	blood:
8	chr12:27091121..27091866-chr15:59981113..59981813,2	Hela-S3	cervix:
9	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
10	chr15:59970781..59973494-chr15:59980091..59981802,2	MCF-7	breast:
11	chr14:24582979..24583595-chr15:59980787..59981641,2	Hela-S3	cervix:
12	chr1:197170147..197170772-chr15:59981162..59981764,2	Hela-S3	cervix:
13	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
14	chr15:59981502..59982267-chr9:7799535..7800195,2	NB4	blood:
15	chr15:59981413..59984505-chr15:60688549..60691597,3	K562	blood:
16	chr15:59395795..59398698-chr15:59981439..59982956,2	K562	blood:
17	chr15:59980114..59982040-chr15:60675665..60677456,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT3-1	chr15:59981276-59981617	ENSG00000259238.1

No data

Variant related genes	Relation type
BNIP2	TF binding region
BNIP2	CpG island
ENSG00000245534	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000155508	Chromatin interaction
ENSG00000111790	Chromatin interaction
ENSG00000100897	Chromatin interaction
ENSG00000064102	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000182718	Chromatin interaction
ENSG00000157456	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000134376	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000137038	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10152791	0.80[AFR][1000 genomes]
rs11071471	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438078	0.88[EUR][1000 genomes]
rs12440020	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442896	0.85[EUR][1000 genomes]
rs12443242	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12443297	0.86[EUR][1000 genomes]
rs12910451	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13380147	0.81[AFR][1000 genomes]
rs16941645	0.83[AFR][1000 genomes]
rs16941648	0.80[AFR][1000 genomes]
rs17236867	0.81[EUR][1000 genomes]
rs1871504	0.87[EUR][1000 genomes]
rs2306357	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306358	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3087328	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3848119	0.82[EUR][1000 genomes]
rs3936513	0.81[EUR][1000 genomes]
rs56141740	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151440	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151441	0.87[EUR][1000 genomes]
rs6151442	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151444	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151445	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151446	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151447	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151448	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151449	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151450	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151451	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6494138	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6494139	0.86[EUR][1000 genomes]
rs67712565	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7173534	0.86[EUR][1000 genomes]
rs7173827	0.86[EUR][1000 genomes]
rs7178211	0.86[EUR][1000 genomes]
rs72625734	0.80[AFR][1000 genomes]
rs728037	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs728038	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs754642	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754643	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs755605	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8025415	0.80[AFR][1000 genomes]
rs8026680	0.80[AFR][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs754641	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs754641	GTF2A2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59979600-59982400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:59979600-59982400	Active TSS	GM12878-XiMat	blood
3	chr15:59979600-59982400	Active TSS	HSMMtube	muscle
4	chr15:59979800-59982400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:59979800-59982400	Active TSS	Left Ventricle	heart
6	chr15:59979800-59982600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr15:59979800-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:59980000-59982200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:59980000-59982200	Active TSS	Colonic Mucosa	Colon
10	chr15:59980000-59982200	Active TSS	Lung	lung
11	chr15:59980000-59982400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:59980000-59982400	Active TSS	Fetal Muscle Trunk	muscle
13	chr15:59980000-59982600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:59980000-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:59980000-59982600	Active TSS	Ovary	ovary
16	chr15:59980200-59982200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:59980200-59982200	Active TSS	Primary monocytes fromperipheralblood	blood
18	chr15:59980200-59982200	Active TSS	Primary B cells from peripheral blood	blood
19	chr15:59980200-59982200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:59980200-59982200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:59980200-59982200	Active TSS	Esophagus	oesophagus
22	chr15:59980200-59982200	Active TSS	Gastric	stomach
23	chr15:59980200-59982200	Bivalent/Poised TSS	HepG2	liver
24	chr15:59980200-59982400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr15:59980200-59982400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:59980200-59982400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:59980200-59982400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:59980200-59982400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:59980200-59982400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:59980200-59982400	Active TSS	Muscle Satellite Cultured Cells	--
31	chr15:59980200-59982400	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr15:59980200-59982400	Active TSS	Psoas Muscle	Psoas
33	chr15:59980200-59982400	Active TSS	HSMM	muscle
34	chr15:59980200-59982400	Active TSS	NHLF	lung
35	chr15:59980200-59982600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:59980200-59982600	Active TSS	Right Ventricle	heart
37	chr15:59980200-59982600	Active TSS	K562	blood
38	chr15:59980200-59982600	Active TSS	NHDF-Ad	bronchial
39	chr15:59980400-59982000	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr15:59980400-59982200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:59980400-59982200	Active TSS	Primary T cells fromperipheralblood	blood
42	chr15:59980400-59982200	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr15:59980400-59982200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:59980400-59982200	Active TSS	Liver	Liver
45	chr15:59980400-59982200	Active TSS	Fetal Thymus	thymus
46	chr15:59980400-59982200	Active TSS	Placenta Amnion	Placenta Amnion
47	chr15:59980400-59982200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr15:59980400-59982200	Active TSS	Stomach Mucosa	stomach
49	chr15:59980400-59982200	Active TSS	HMEC	breast
50	chr15:59980400-59982200	Active TSS	HUVEC	blood vessel

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