Variant report

Variant	rs6151440
Chromosome Location	chr15:59980635-59980636
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:120)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:120 , 50 per page) page: 1 2 3

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	MAX	chr15:59980606-59982493	A549	lung:	n/a	n/a
4	TBP	chr15:59980282-59981042	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:59980593-59980898	GM12891	blood:	n/a	n/a
6	ELK1	chr15:59980051-59980863	K562	blood:	n/a	chr15:59980291-59980300 chr15:59980291-59980300
7	POLR2A	chr15:59980050-59982314	NB4	blood:	n/a	n/a
8	TAF1	chr15:59980581-59980969	H1-neurons	neurons:	n/a	n/a
9	BRCA1	chr15:59980439-59982136	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr15:59980247-59981945	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr15:59980389-59982367	Hela-S3	cervix:	n/a	n/a
12	IRF1	chr15:59980085-59981955	K562	blood:	n/a	chr15:59981805-59981819 chr15:59981815-59981828
13	CTCF	chr15:59980032-59984022	A549	lung:	n/a	n/a
14	POLR2A	chr15:59980628-59982340	SK-N-MC	brain:	n/a	n/a
15	SP1	chr15:59980612-59982340	A549	lung:	n/a	chr15:59981709-59981720
16	POLR2A	chr15:59980521-59981988	SK-N-SH	brain:	n/a	n/a
17	ELF1	chr15:59980568-59981902	MCF-7	breast:	n/a	n/a
18	POLR2A	chr15:59980621-59982035	K562	blood:	n/a	n/a
19	RUNX3	chr15:59980558-59981924	GM12878	blood:	n/a	n/a
20	POLR2A	chr15:59979986-59982227	GM12878	blood:	n/a	n/a
21	GABPA	chr15:59979737-59981942	A549	lung:	n/a	n/a
22	GATA2	chr15:59980022-59980745	HUVEC	blood vessel:	n/a	n/a
23	ELK1	chr15:59980029-59981849	GM12878	blood:	n/a	chr15:59980291-59980300 chr15:59980291-59980300
24	POLR2A	chr15:59979315-59982513	MCF10A-Er-Src	breast:	n/a	n/a
25	ELF1	chr15:59980567-59981687	HepG2	liver:	n/a	n/a
26	PML	chr15:59980471-59982000	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:59980606-59982009	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr15:59980617-59981879	PANC-1	pancreas:	n/a	n/a
29	MXI1	chr15:59979968-59982637	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr15:59979869-59982333	HUVEC	blood vessel:	n/a	n/a
31	REST	chr15:59980481-59982028	H1-neurons	neurons:	n/a	n/a
32	GABPA	chr15:59980606-59981892	HL-60	blood:	n/a	n/a
33	MYC	chr15:59980601-59980949	MCF10A-Er-Src	breast:	n/a	n/a
34	CEBPB	chr15:59980506-59981061	Hela-S3	cervix:	n/a	n/a
35	TCF12	chr15:59980542-59982638	A549	lung:	n/a	n/a
36	SIN3AK20	chr15:59980566-59981070	A549	lung:	n/a	n/a
37	ELF1	chr15:59980516-59981325	A549	lung:	n/a	n/a
38	GABPA	chr15:59980451-59981910	A549	lung:	n/a	n/a
39	TAF1	chr15:59980577-59981918	K562	blood:	n/a	n/a
40	RCOR1	chr15:59980601-59982194	Hela-S3	cervix:	n/a	n/a
41	IRF1	chr15:59980498-59981189	K562	blood:	n/a	n/a
42	SIN3A	chr15:59980635-59982050	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr15:59979865-59982169	GM12891	blood:	n/a	n/a
44	POLR2A	chr15:59980570-59981885	GM12892	blood:	n/a	n/a
45	SIN3AK20	chr15:59980555-59981022	K562	blood:	n/a	n/a
46	MYC	chr15:59980578-59982317	K562	blood:	n/a	n/a
47	POLR2A	chr15:59980581-59982274	HUVEC	blood vessel:	n/a	n/a
48	CHD1	chr15:59980233-59980938	GM12878	blood:	n/a	n/a
49	TBP	chr15:59980577-59981814	HepG2	liver:	n/a	n/a
50	POLR2A	chr15:59980589-59982400	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59979537..59981515-chr15:60770595..60772119,2	K562	blood:
2	chr15:59979548..59984505-chr15:60688391..60691990,7	K562	blood:
3	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:
4	chr15:59979537..59982042-chr15:60770595..60772312,3	K562	blood:
5	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
6	chr15:59970781..59973494-chr15:59980091..59981802,2	MCF-7	breast:
7	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
8	chr15:59980562..59981496-chr9:33024819..33025373,2	Hela-S3	cervix:
9	chr15:59979503..59981285-chr3:183330477..183331977,2	K562	blood:
10	chr15:59980114..59982040-chr15:60675665..60677456,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259238	TF binding region
ENSG00000182718	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000243584	Chromatin interaction
ENSG00000137074	Chromatin interaction
ENSG00000086061	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1002181	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10162629	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1046053	0.83[ASN][1000 genomes]
rs11071468	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11071469	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11071471	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11629681	0.80[EUR][1000 genomes]
rs11634157	0.82[EUR][1000 genomes]
rs12438078	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12439645	0.81[EUR][1000 genomes]
rs12439658	0.80[EUR][1000 genomes]
rs12439707	0.80[EUR][1000 genomes]
rs12440020	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442896	0.88[EUR][1000 genomes]
rs12443242	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12443297	0.89[EUR][1000 genomes]
rs12593480	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12903647	0.83[ASN][1000 genomes]
rs12904505	0.82[EUR][1000 genomes]
rs12907554	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12910451	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1552031	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17191002	0.80[EUR][1000 genomes]
rs17236804	0.85[ASN][1000 genomes]
rs17236867	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1871504	0.90[EUR][1000 genomes]
rs2306357	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306358	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307272	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2307275	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3087328	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3843695	0.83[EUR][1000 genomes]
rs3848119	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3936513	0.84[EUR][1000 genomes]
rs4533213	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4774340	0.80[ASN][1000 genomes]
rs4775195	0.83[ASN][1000 genomes]
rs4775200	0.82[EUR][1000 genomes]
rs56141740	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151441	0.90[EUR][1000 genomes]
rs6151442	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151444	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151445	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151446	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151447	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151448	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151449	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151450	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151451	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151458	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151459	0.82[ASN][1000 genomes]
rs6151460	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151461	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151462	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151467	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151470	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151472	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151474	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151477	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6151486	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6151491	0.85[ASN][1000 genomes]
rs6151494	0.85[ASN][1000 genomes]
rs6151496	0.85[ASN][1000 genomes]
rs6151501	0.84[ASN][1000 genomes]
rs6151503	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151504	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151506	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151514	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151528	0.82[ASN][1000 genomes]
rs6151529	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151532	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151533	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151535	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151536	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151542	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151545	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6494133	0.83[ASN][1000 genomes]
rs6494138	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494139	0.89[EUR][1000 genomes]
rs6494140	0.82[EUR][1000 genomes]
rs67712565	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67820349	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7162645	0.82[EUR][1000 genomes]
rs7173534	0.89[EUR][1000 genomes]
rs7173827	0.89[EUR][1000 genomes]
rs7178211	0.89[EUR][1000 genomes]
rs722163	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs722164	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs728037	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs728038	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754641	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs754642	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754643	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs755605	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	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
rs6151440	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs6151440	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	chr15:59977200-59981000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:59977800-59980800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:59977800-59981000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr15:59978200-59981000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr15:59979600-59980800	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr15:59979600-59981200	Active TSS	Right Atrium	heart
7	chr15:59979600-59982400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:59979600-59982400	Active TSS	GM12878-XiMat	blood
9	chr15:59979600-59982400	Active TSS	HSMMtube	muscle
10	chr15:59979800-59980800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr15:59979800-59982400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr15:59979800-59982400	Active TSS	Left Ventricle	heart
13	chr15:59979800-59982600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr15:59979800-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:59980000-59980800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:59980000-59982200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:59980000-59982200	Active TSS	Colonic Mucosa	Colon
18	chr15:59980000-59982200	Active TSS	Lung	lung
19	chr15:59980000-59982400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:59980000-59982400	Active TSS	Fetal Muscle Trunk	muscle
21	chr15:59980000-59982600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:59980000-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:59980000-59982600	Active TSS	Ovary	ovary
24	chr15:59980200-59981200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:59980200-59982200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:59980200-59982200	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr15:59980200-59982200	Active TSS	Primary B cells from peripheral blood	blood
28	chr15:59980200-59982200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:59980200-59982200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:59980200-59982200	Active TSS	Esophagus	oesophagus
31	chr15:59980200-59982200	Active TSS	Gastric	stomach
32	chr15:59980200-59982200	Bivalent/Poised TSS	HepG2	liver
33	chr15:59980200-59982400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr15:59980200-59982400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:59980200-59982400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:59980200-59982400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:59980200-59982400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:59980200-59982400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:59980200-59982400	Active TSS	Muscle Satellite Cultured Cells	--
40	chr15:59980200-59982400	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr15:59980200-59982400	Active TSS	Psoas Muscle	Psoas
42	chr15:59980200-59982400	Active TSS	HSMM	muscle
43	chr15:59980200-59982400	Active TSS	NHLF	lung
44	chr15:59980200-59982600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:59980200-59982600	Active TSS	Right Ventricle	heart
46	chr15:59980200-59982600	Active TSS	K562	blood
47	chr15:59980200-59982600	Active TSS	NHDF-Ad	bronchial
48	chr15:59980400-59980800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:59980400-59981000	Active TSS	Brain Germinal Matrix	brain
50	chr15:59980400-59981000	Active TSS	Fetal Brain Female	brain

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