Variant report

Variant	rs755605
Chromosome Location	chr15:59982419-59982420
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:59980606-59982493	A549	lung:	n/a	n/a
2	CTCF	chr15:59980032-59984022	A549	lung:	n/a	n/a
3	POLR2A	chr15:59979315-59982513	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr15:59979968-59982637	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr15:59980542-59982638	A549	lung:	n/a	n/a
6	BACH1	chr15:59982395-59982493	K562	blood:	n/a	n/a
7	POLR2A	chr15:59980602-59982423	K562	blood:	n/a	n/a
8	GATA1	chr15:59979887-59982469	PBDE	blood:	n/a	n/a
9	HCFC1	chr15:59980047-59982663	Hela-S3	cervix:	n/a	n/a
10	EGR1	chr15:59981093-59982471	HCT-116	colon:	n/a	chr15:59981601-59981615 chr15:59981584-59981598
11	JUN	chr15:59979681-59982479	K562	blood:	n/a	n/a
12	POLR2A	chr15:59979872-59982471	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA2	chr15:59981915-59982430	A549	lung:	n/a	n/a
14	POLR2A	chr15:59979846-59982515	PBDE	blood:	n/a	n/a
15	MAZ	chr15:59979931-59982669	IMR90	lung:	n/a	n/a
16	EGR1	chr15:59980776-59982478	HCT-116	colon:	n/a	chr15:59981601-59981615 chr15:59981584-59981598

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:59982396-59982446	MCF10A-Er-Src	breast:	n/a
2	chr15:59982396-59982446	ProgFib	skin:	n/a
3	chr15:59982396-59982446	SK-N-MC	brain:	n/a
4	chr15:59982396-59982446	A549	lung:	n/a
5	chr15:59982396-59982446	HNPCEpiC	eye:	n/a
6	chr15:59982396-59982446	HepG2	liver:	n/a
7	chr15:59982396-59982446	HEEpiC	esophagus:	n/a
8	chr15:59982396-59982446	HRE	kidney:	n/a
9	chr15:59982396-59982446	AG09319	gingival:	n/a
10	chr15:59982396-59982446	PFSK-1	brain:	n/a
11	chr15:59982396-59982446	LNCaP	prostate:	n/a
12	chr15:59982396-59982446	AoSMC	blood vessel:	n/a
13	chr15:59982396-59982446	SAEC	small airway:	n/a
14	chr15:59982396-59982446	NHDF-neo	bronchial:	n/a
15	chr15:59982396-59982446	HIPEpiC	eye:	n/a
16	chr15:59982396-59982446	PANC-1	pancreas:	n/a
17	chr15:59982396-59982446	GM12878	blood:	n/a
18	chr15:59982396-59982446	HUVEC	blood vessel:	n/a
19	chr15:59982396-59982446	ovcar-3	ovarian:	n/a
20	chr15:59982396-59982446	HCM	heart:	n/a
21	chr15:59982396-59982446	SKMC	muscle:	n/a
22	chr15:59982396-59982446	HMEC	breast:	n/a
23	chr15:59982396-59982446	HPAEpiC	pulmonary alveolar:	n/a
24	chr15:59982396-59982446	AG04450	lung:	fetal
25	chr15:59982396-59982446	T-47D	breast:	n/a
26	chr15:59982396-59982446	NH-A	brain:	n/a
27	chr15:59982396-59982446	HCPEpiC	choroid plexus:	n/a
28	chr15:59982396-59982446	CMK	blood:	n/a
29	chr15:59982396-59982446	SK-N-SH_RA	brain:	n/a
30	chr15:59982396-59982446	IMR90	lung:	fetal
31	chr15:59982396-59982446	BE2_C	brain:	n/a
32	chr15:59982396-59982446	SK-N-SH	brain:	n/a
33	chr15:59982396-59982446	HEK293	kidney:	embryo
34	chr15:59982396-59982446	Hepatocyte	liver:	n/a
35	chr15:59982396-59982446	HL-60	blood:	n/a
36	chr15:59982396-59982446	GM19239	blood:	n/a
37	chr15:59982396-59982446	RPTEC	kidney:	n/a
38	chr15:59982396-59982446	U87	brain:	n/a
39	chr15:59982396-59982446	K562	blood:	n/a
40	chr15:59982396-59982446	GM12891	blood:	n/a
41	chr15:59982396-59982446	HAEpiC	amniotic membrane:	n/a
42	chr15:59982396-59982446	HRCEpiC	kidney:	n/a
43	chr15:59982396-59982446	AG09309	skin:	n/a
44	chr15:59982396-59982446	AG10803	skin:	n/a
45	chr15:59982396-59982446	NHBE	bronchial:	n/a
46	chr15:59982396-59982446	Jurkat	blood:	n/a
47	chr15:59982396-59982446	Hela-S3	cervix:	n/a
48	chr15:59982396-59982446	NB4	blood:	n/a
49	chr15:59982396-59982446	BJ	skin:	n/a
50	chr15:59982396-59982446	HRPEpiC	eye:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59981055..59982632-chr15:60666693..60668743,2	MCF-7	breast:
2	chr15:59979548..59984505-chr15:60688391..60691990,7	K562	blood:
3	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:
4	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
5	chr15:59981413..59984505-chr15:60688549..60691597,3	K562	blood:
6	chr15:59395795..59398698-chr15:59981439..59982956,2	K562	blood:

No data

Variant related genes	Relation type
BNIP2	TF binding region
BNIP2	CpG island
ENSG00000182718	Chromatin interaction
ENSG00000157456	Chromatin interaction
ENSG00000140307	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1002181	0.83[ASN][1000 genomes]
rs10152431	0.83[AFR][1000 genomes]
rs10152791	0.83[AFR][1000 genomes]
rs10162629	0.83[ASN][1000 genomes]
rs1046053	0.82[ASN][1000 genomes]
rs11071468	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11071469	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11071471	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11629681	0.80[EUR][1000 genomes]
rs11634157	0.82[EUR][1000 genomes]
rs12438078	0.81[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	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442896	0.88[EUR][1000 genomes]
rs12443242	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443297	0.89[EUR][1000 genomes]
rs12593480	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12903647	0.82[ASN][1000 genomes]
rs12904505	0.82[EUR][1000 genomes]
rs12907554	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12910451	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379702	0.83[AFR][1000 genomes]
rs13380147	0.84[AFR][1000 genomes]
rs1552031	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16941645	0.86[AFR][1000 genomes]
rs16941648	0.83[AFR][1000 genomes]
rs17191002	0.80[EUR][1000 genomes]
rs17236804	0.85[ASN][1000 genomes]
rs17236867	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1871504	0.90[EUR][1000 genomes]
rs2306357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307272	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2307275	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3087328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843695	0.83[EUR][1000 genomes]
rs3848119	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3936513	0.84[EUR][1000 genomes]
rs4533213	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4775195	0.82[ASN][1000 genomes]
rs4775200	0.82[EUR][1000 genomes]
rs56141740	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151440	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151441	0.90[EUR][1000 genomes]
rs6151442	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151444	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151445	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151446	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151447	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151448	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151449	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151450	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151451	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151458	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151459	0.81[ASN][1000 genomes]
rs6151460	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151461	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151462	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6151467	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151470	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151472	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151474	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151477	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6151486	0.81[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	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151504	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151506	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151514	0.83[ASN][1000 genomes]
rs6151528	0.81[ASN][1000 genomes]
rs6151529	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6151532	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6151533	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6151535	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6151536	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6151542	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6151545	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6494133	0.82[ASN][1000 genomes]
rs6494138	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494139	0.89[EUR][1000 genomes]
rs6494140	0.82[EUR][1000 genomes]
rs67712565	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67820349	0.82[AMR][1000 genomes];0.83[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	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs722164	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72625734	0.83[AFR][1000 genomes]
rs728037	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs728038	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754641	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs754642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025415	0.83[AFR][1000 genomes]
rs8026680	0.83[AFR][1000 genomes]
rs8027353	0.82[AFR][1000 genomes]
rs8027389	0.82[AFR][1000 genomes]
rs8027415	0.82[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
rs755605	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL
rs755605	GTF2A2	cis	Whole Blood	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59979800-59982600	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:59979800-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:59980000-59982600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:59980000-59982600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:59980000-59982600	Active TSS	Ovary	ovary
6	chr15:59980200-59982600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:59980200-59982600	Active TSS	Right Ventricle	heart
8	chr15:59980200-59982600	Active TSS	K562	blood
9	chr15:59980200-59982600	Active TSS	NHDF-Ad	bronchial
10	chr15:59980400-59982600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr15:59980400-59982600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr15:59980400-59982600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr15:59980400-59982600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:59980400-59982600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr15:59980400-59982600	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr15:59980400-59982600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:59980400-59982600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:59980400-59982600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:59980400-59982600	Active TSS	Aorta	Aorta
20	chr15:59980400-59982600	Active TSS	Fetal Intestine Large	intestine
21	chr15:59980400-59982600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr15:59980400-59982600	Active TSS	Thymus	Thymus
23	chr15:59980400-59982800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr15:59980600-59982600	Active TSS	Rectal Smooth Muscle	rectum
25	chr15:59980600-59982600	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr15:59980600-59982600	Active TSS	Stomach Smooth Muscle	stomach
27	chr15:59981800-59982600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr15:59981800-59982800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr15:59982000-59982800	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr15:59982000-59982800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr15:59982200-59982600	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr15:59982200-59982600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr15:59982200-59982600	Flanking Active TSS	Fetal Thymus	thymus
34	chr15:59982200-59982600	Flanking Active TSS	HMEC	breast
35	chr15:59982200-59982600	Flanking Active TSS	HUVEC	blood vessel
36	chr15:59982200-59982600	Flanking Active TSS	NHEK	skin
37	chr15:59982200-59982600	Flanking Active TSS	Osteobl	bone
38	chr15:59982200-59982800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:59982200-59982800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:59982200-59982800	Flanking Active TSS	Liver	Liver
41	chr15:59982200-59983200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:59982200-59983400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:59982200-59983400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr15:59982200-59986600	Weak transcription	Stomach Mucosa	stomach
45	chr15:59982400-59982600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:59982400-59982600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:59982400-59982600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:59982400-59982600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr15:59982400-59982600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr15:59982400-59982600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell

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