Variant report

Variant	rs4533213
Chromosome Location	chr15:59975082-59975083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59974949..59977182-chr15:59979854..59981914,2	MCF-7	breast:
2	chr15:59947943..59950791-chr15:59975070..59977173,2	K562	blood:

Variant related genes	Relation type
ENSG00000140299	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000259238	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs1002181	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10152209	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152373	0.86[AFR][1000 genomes]
rs10152414	0.93[EUR][1000 genomes]
rs10152415	0.93[EUR][1000 genomes]
rs10152509	0.83[EUR][1000 genomes]
rs10162629	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1046053	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519039	0.85[AFR][1000 genomes]
rs1057059	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11071465	0.94[EUR][1000 genomes]
rs11071468	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071469	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071471	0.80[ASN][1000 genomes]
rs1135148	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634067	0.92[EUR][1000 genomes]
rs11637071	0.84[EUR][1000 genomes]
rs11637359	0.83[EUR][1000 genomes]
rs11853610	0.91[EUR][1000 genomes]
rs11854063	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12440020	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12441240	0.94[EUR][1000 genomes]
rs12443242	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12593480	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12708458	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12708459	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12902582	0.93[EUR][1000 genomes]
rs12903647	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906392	0.92[EUR][1000 genomes]
rs12907554	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12907641	0.85[EUR][1000 genomes]
rs12909005	0.83[EUR][1000 genomes]
rs12910451	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12912652	0.88[EUR][1000 genomes]
rs1479885	0.84[EUR][1000 genomes]
rs1531638	0.87[EUR][1000 genomes]
rs1531639	0.87[EUR][1000 genomes]
rs1552031	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236804	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1871499	0.87[EUR][1000 genomes]
rs1871500	0.94[EUR][1000 genomes]
rs1871503	0.88[EUR][1000 genomes]
rs1979422	0.81[EUR][1000 genomes]
rs2101019	0.84[EUR][1000 genomes]
rs2170062	0.80[EUR][1000 genomes]
rs2306355	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2306357	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2306358	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2307272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307273	0.86[EUR][1000 genomes]
rs2307275	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28671744	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899649	0.88[EUR][1000 genomes]
rs3087328	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34797071	0.92[EUR][1000 genomes]
rs34894301	0.90[EUR][1000 genomes]
rs3784389	0.92[EUR][1000 genomes]
rs3825870	0.87[EUR][1000 genomes]
rs4232	0.80[EUR][1000 genomes]
rs4270113	0.87[EUR][1000 genomes]
rs4774340	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774341	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775191	0.89[EUR][1000 genomes]
rs4775195	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4775197	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56141740	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58190651	0.84[AFR][1000 genomes]
rs6151440	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6151442	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151444	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151445	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151446	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151447	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6151448	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151449	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151450	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151451	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6151458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151459	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151462	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151464	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6151467	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151472	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151483	0.89[EUR][1000 genomes]
rs6151486	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151487	0.89[EUR][1000 genomes]
rs6151491	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6151494	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6151496	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6151501	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151506	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151510	0.82[EUR][1000 genomes]
rs6151514	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151525	0.88[EUR][1000 genomes]
rs6151528	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151529	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151532	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151533	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151535	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151536	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151542	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151545	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151551	0.88[EUR][1000 genomes]
rs6151553	0.88[EUR][1000 genomes]
rs6151557	0.85[EUR][1000 genomes]
rs6151561	0.86[EUR][1000 genomes]
rs6151565	0.86[EUR][1000 genomes]
rs6151568	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151570	0.86[EUR][1000 genomes]
rs6151571	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151574	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151576	0.86[EUR][1000 genomes]
rs6151580	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151581	0.92[EUR][1000 genomes]
rs6151586	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151588	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151589	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151590	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151592	0.87[EUR][1000 genomes]
rs62012358	0.87[EUR][1000 genomes]
rs62015260	0.81[EUR][1000 genomes]
rs62015289	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6494128	0.87[EUR][1000 genomes]
rs6494130	0.87[EUR][1000 genomes]
rs6494131	0.93[EUR][1000 genomes]
rs6494133	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494138	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67697180	0.82[EUR][1000 genomes]
rs67820349	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7162964	0.86[EUR][1000 genomes]
rs7164756	0.93[EUR][1000 genomes]
rs7178050	0.87[EUR][1000 genomes]
rs7180408	0.93[EUR][1000 genomes]
rs7182962	0.91[EUR][1000 genomes]
rs722163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs722164	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728037	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs728038	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs74017838	0.85[AFR][1000 genomes]
rs7497974	0.88[EUR][1000 genomes]
rs754642	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs754643	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs755605	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7882	0.87[EUR][1000 genomes]
rs8033161	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8040114	0.86[EUR][1000 genomes]
rs8041394	0.94[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4533213	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	chr15:59951000-59978400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:59951400-59975200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:59951400-59975400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr15:59951400-59976000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:59951400-59978800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:59951600-59976400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr15:59951800-59975600	Strong transcription	Primary B cells from cord blood	blood
10	chr15:59952000-59975600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:59952000-59976600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:59952000-59977800	Strong transcription	Hela-S3	cervix
13	chr15:59952200-59975400	Strong transcription	Fetal Thymus	thymus
14	chr15:59952200-59975600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:59952200-59976400	Strong transcription	Placenta	Placenta
16	chr15:59952400-59975800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:59952400-59977400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr15:59952400-59978600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:59952600-59975600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr15:59952600-59976000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:59952600-59976800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:59952800-59977400	Strong transcription	Dnd41	blood
23	chr15:59954200-59975200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:59956200-59975600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:59956600-59975600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:59957000-59975600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:59957800-59977200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:59959600-59975400	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:59959800-59975600	Strong transcription	GM12878-XiMat	blood
30	chr15:59960600-59975400	Strong transcription	NHEK	skin
31	chr15:59960800-59976200	Strong transcription	NHDF-Ad	bronchial
32	chr15:59961600-59975600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:59961600-59976800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:59962000-59979400	Weak transcription	Fetal Heart	heart
35	chr15:59965000-59980200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:59966400-59976400	Strong transcription	K562	blood
37	chr15:59966600-59976000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr15:59967200-59976200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:59967800-59975200	Strong transcription	Liver	Liver
40	chr15:59968000-59976400	Strong transcription	NHLF	lung
41	chr15:59968200-59979600	Weak transcription	Fetal Brain Male	brain
42	chr15:59969600-59977600	Weak transcription	Stomach Mucosa	stomach
43	chr15:59969600-59978400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:59969600-59980000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:59969800-59976800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:59970200-59976000	Weak transcription	Small Intestine	intestine
47	chr15:59970200-59978400	Weak transcription	Psoas Muscle	Psoas
48	chr15:59970600-59979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:59970800-59979800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:59971600-59975800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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