Variant report

Variant	rs8040114
Chromosome Location	chr15:59957585-59957586
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	chr15:59949353..59952848-chr15:59957415..59960661,3	MCF-7	breast:
2	chr15:59956676..59958590-chr15:59980762..59982433,2	K562	blood:

Variant related genes	Relation type
ENSG00000140307	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1002181	0.87[EUR][1000 genomes]
rs10152209	0.85[EUR][1000 genomes]
rs10152414	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10152415	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10152509	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10162629	0.88[EUR][1000 genomes]
rs1046053	0.87[EUR][1000 genomes]
rs1057059	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11071465	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11071468	0.88[EUR][1000 genomes]
rs11071469	0.88[EUR][1000 genomes]
rs1135148	0.83[EUR][1000 genomes]
rs11634067	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11637071	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637359	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11853610	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11854063	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12441240	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12593480	0.88[EUR][1000 genomes]
rs12708458	0.83[EUR][1000 genomes]
rs12708459	0.84[EUR][1000 genomes]
rs12902582	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12902774	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903647	0.83[EUR][1000 genomes]
rs12906392	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907554	0.87[EUR][1000 genomes]
rs12907641	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12909005	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912652	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531638	0.81[EUR][1000 genomes]
rs1531639	0.80[EUR][1000 genomes]
rs1552031	0.87[EUR][1000 genomes]
rs1871499	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871500	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1871503	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979422	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2101019	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2170062	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2306354	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2306355	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2307272	0.87[EUR][1000 genomes]
rs2307273	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307275	0.86[EUR][1000 genomes]
rs2414638	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28671744	0.85[EUR][1000 genomes]
rs2899649	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34797071	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34894301	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3825870	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4270113	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4533213	0.86[EUR][1000 genomes]
rs4774340	0.84[EUR][1000 genomes]
rs4774341	0.85[EUR][1000 genomes]
rs4775191	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4775195	0.87[EUR][1000 genomes]
rs4775197	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151458	0.86[EUR][1000 genomes]
rs6151459	0.81[EUR][1000 genomes]
rs6151460	0.86[EUR][1000 genomes]
rs6151461	0.86[EUR][1000 genomes]
rs6151462	0.86[EUR][1000 genomes]
rs6151467	0.86[EUR][1000 genomes]
rs6151470	0.86[EUR][1000 genomes]
rs6151472	0.85[EUR][1000 genomes]
rs6151474	0.86[EUR][1000 genomes]
rs6151477	0.86[EUR][1000 genomes]
rs6151483	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151486	0.86[EUR][1000 genomes]
rs6151487	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151501	0.85[EUR][1000 genomes]
rs6151503	0.87[EUR][1000 genomes]
rs6151504	0.87[EUR][1000 genomes]
rs6151506	0.87[EUR][1000 genomes]
rs6151510	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151514	0.86[EUR][1000 genomes]
rs6151525	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151528	0.86[EUR][1000 genomes]
rs6151529	0.86[EUR][1000 genomes]
rs6151532	0.86[EUR][1000 genomes]
rs6151533	0.87[EUR][1000 genomes]
rs6151535	0.88[EUR][1000 genomes]
rs6151536	0.88[EUR][1000 genomes]
rs6151542	0.88[EUR][1000 genomes]
rs6151545	0.88[EUR][1000 genomes]
rs6151551	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151553	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151557	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151561	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151565	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151568	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151570	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151571	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151574	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6151576	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151580	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6151581	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151586	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151588	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151589	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151590	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151592	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62012358	0.80[EUR][1000 genomes]
rs62015260	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62015289	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6494127	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6494128	0.81[EUR][1000 genomes]
rs6494130	0.81[EUR][1000 genomes]
rs6494131	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6494133	0.87[EUR][1000 genomes]
rs67697180	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67820349	0.87[EUR][1000 genomes]
rs7164756	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7172270	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178050	0.80[EUR][1000 genomes]
rs7180408	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7182962	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs722163	0.86[EUR][1000 genomes]
rs722164	0.86[EUR][1000 genomes]
rs7497974	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7882	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8033161	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8035465	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8041394	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8040114	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59949400-59960200	Weak transcription	Fetal Heart	heart
2	chr15:59949800-59963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:59949800-59964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:59949800-59968000	Weak transcription	Stomach Mucosa	stomach
5	chr15:59949800-59968400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:59950000-59963200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:59950200-59958400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:59950200-59959200	Weak transcription	Fetal Brain Male	brain
10	chr15:59950200-59960200	Weak transcription	Colonic Mucosa	Colon
11	chr15:59950200-59961200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:59950200-59963400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:59950200-59963400	Weak transcription	Brain Angular Gyrus	brain
14	chr15:59950200-59963400	Weak transcription	Ovary	ovary
15	chr15:59950200-59964000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:59950200-59964000	Weak transcription	Gastric	stomach
17	chr15:59950200-59964000	Weak transcription	Lung	lung
18	chr15:59950200-59964000	Weak transcription	Small Intestine	intestine
19	chr15:59950200-59967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:59950200-59968400	Weak transcription	Right Ventricle	heart
21	chr15:59950200-59968800	Weak transcription	Aorta	Aorta
22	chr15:59950400-59958400	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:59950400-59960200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:59950400-59964000	Weak transcription	Pancreas	Pancrea
25	chr15:59950400-59964000	Weak transcription	Psoas Muscle	Psoas
26	chr15:59950400-59965600	Weak transcription	Brain Substantia Nigra	brain
27	chr15:59950400-59968800	Weak transcription	Esophagus	oesophagus
28	chr15:59950400-59979600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:59950600-59957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:59950800-59961600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:59951000-59978400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:59951200-59958600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:59951400-59960600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:59951400-59964600	Strong transcription	HUVEC	blood vessel
35	chr15:59951400-59965400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr15:59951400-59972600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:59951400-59973600	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr15:59951400-59973600	Strong transcription	HSMM	muscle
39	chr15:59951400-59975000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:59951400-59975200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:59951400-59975400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr15:59951400-59976000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:59951400-59978800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:59951600-59976400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr15:59951800-59975000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:59951800-59975600	Strong transcription	Primary B cells from cord blood	blood
47	chr15:59952000-59975600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:59952000-59976600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr15:59952000-59977800	Strong transcription	Hela-S3	cervix
50	chr15:59952200-59959000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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