Variant report

Variant	rs728038
Chromosome Location	chr15:59979446-59979447
allele	A/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	POLR2A	chr15:59979315-59982513	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:59979384-59979805	HepG2	liver:	n/a	n/a
3	MAFK	chr15:59979279-59979450	HepG2	liver:	n/a	chr15:59979369-59979380 chr15:59979370-59979381 chr15:59979368-59979382 chr15:59979370-59979381 chr15:59979369-59979380

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:

Variant related genes	Relation type
ENSG00000259238	TF binding region
BNIP2	TF binding region
ENSG00000140307	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	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10152209	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10152373	0.84[AFR][1000 genomes]
rs10162629	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1046053	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10519039	0.83[AFR][1000 genomes]
rs11071468	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11071469	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11071471	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1135148	0.88[ASN][1000 genomes]
rs12438078	0.89[EUR][1000 genomes]
rs12440020	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12442896	0.85[EUR][1000 genomes]
rs12443242	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12443297	0.87[EUR][1000 genomes]
rs12593480	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12708458	0.88[ASN][1000 genomes]
rs12708459	0.87[ASN][1000 genomes]
rs12903647	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12907554	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12910451	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1552031	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17236804	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17236867	0.82[EUR][1000 genomes]
rs1871504	0.88[EUR][1000 genomes]
rs2306357	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306358	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2307272	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2307275	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28671744	0.84[ASN][1000 genomes]
rs3087328	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3843695	0.81[EUR][1000 genomes]
rs3848119	0.83[EUR][1000 genomes]
rs3936513	0.82[EUR][1000 genomes]
rs4533213	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4774340	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4774341	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4775195	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56141740	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58190651	0.82[AFR][1000 genomes]
rs6151440	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151441	0.88[EUR][1000 genomes]
rs6151442	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151444	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151445	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151446	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151447	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151448	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151449	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151450	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151451	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151458	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6151459	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6151460	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6151461	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6151462	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6151464	0.82[ASN][1000 genomes]
rs6151467	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6151470	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6151472	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6151474	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6151477	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6151486	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6151491	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6151494	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6151496	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6151501	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151503	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6151504	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6151506	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6151514	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151528	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6151529	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151532	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151533	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151535	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151536	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151542	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6151545	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6494133	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6494138	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494139	0.87[EUR][1000 genomes]
rs67820349	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7173534	0.87[EUR][1000 genomes]
rs7173827	0.87[EUR][1000 genomes]
rs7178211	0.87[EUR][1000 genomes]
rs722163	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs722164	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs728037	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74017838	0.83[AFR][1000 genomes]
rs754641	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs754642	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754643	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755605	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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
rs728038	GTF2A2	cis	Whole Blood	GTEx
rs728038	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:59950400-59979600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:59965000-59980200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:59968200-59979600	Weak transcription	Fetal Brain Male	brain
5	chr15:59969600-59980000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:59970600-59979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:59970800-59979800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:59973200-59979600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:59973400-59980000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:59973600-59980000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:59973600-59980000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:59973600-59980000	Weak transcription	Esophagus	oesophagus
13	chr15:59973800-59979600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:59973800-59979600	Weak transcription	Brain Angular Gyrus	brain
15	chr15:59974000-59979600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:59974000-59979800	Weak transcription	Fetal Brain Female	brain
17	chr15:59974400-59979600	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:59974400-59979600	Weak transcription	Ovary	ovary
19	chr15:59974400-59979600	Weak transcription	Spleen	Spleen
20	chr15:59974400-59980000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr15:59974400-59980000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:59974400-59980000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:59974400-59980000	Weak transcription	Lung	lung
24	chr15:59974600-59979800	Weak transcription	Fetal Stomach	stomach
25	chr15:59974600-59980000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:59974800-59979600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:59974800-59979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:59974800-59979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:59975000-59979800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:59975200-59979600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:59976200-59979800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr15:59976400-59980400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:59976600-59979600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:59976600-59979800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:59976600-59979800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr15:59976600-59979800	Enhancers	NHDF-Ad	bronchial
37	chr15:59977000-59980400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr15:59977200-59979600	Enhancers	Adipose Nuclei	Adipose
39	chr15:59977200-59981000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:59977400-59979600	Enhancers	Duodenum Mucosa	Duodenum
41	chr15:59977400-59979800	Enhancers	Left Ventricle	heart
42	chr15:59977400-59980000	Enhancers	Gastric	stomach
43	chr15:59977400-59980000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr15:59977600-59979600	Genic enhancers	Dnd41	blood
45	chr15:59977600-59979800	Enhancers	Primary B cells from peripheral blood	blood
46	chr15:59977600-59979800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr15:59977600-59980000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr15:59977600-59980200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:59977800-59979600	Flanking Active TSS	GM12878-XiMat	blood
50	chr15:59977800-59979600	Genic enhancers	HSMM	muscle

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