Variant report

Variant	rs12441240
Chromosome Location	chr15:59943367-59943368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59941827..59945958-chr15:59947356..59950499,4	MCF-7	breast:
2	chr15:59932328..59933962-chr15:59943086..59945341,2	K562	blood:
3	chr15:59942263..59944569-chr15:59959864..59962554,2	K562	blood:
4	chr15:59940140..59943564-chr15:59947807..59951732,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140307	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1002181	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10152209	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10152414	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10152415	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10152509	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10162629	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1046053	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1057059	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11071465	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071468	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11071469	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1135148	0.92[EUR][1000 genomes]
rs11634067	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637071	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11637359	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11853610	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11854063	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593480	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12708458	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12708459	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902582	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902774	0.82[EUR][1000 genomes]
rs12903647	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12906392	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907554	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12907641	0.89[EUR][1000 genomes]
rs12909005	0.88[EUR][1000 genomes]
rs12910751	0.85[EUR][1000 genomes]
rs12912652	0.87[EUR][1000 genomes]
rs1479885	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1531638	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1531639	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552031	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1871499	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1871500	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871503	0.86[EUR][1000 genomes]
rs1979422	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2101019	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2170062	0.85[EUR][1000 genomes]
rs2306355	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2307272	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2307273	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2307275	0.94[EUR][1000 genomes]
rs2414638	0.83[EUR][1000 genomes]
rs28671744	0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2899649	0.87[EUR][1000 genomes]
rs34797071	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34894301	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784389	0.86[EUR][1000 genomes]
rs3825870	0.82[EUR][1000 genomes]
rs4232	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4270113	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4533213	0.94[EUR][1000 genomes]
rs4774340	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4774341	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775191	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4775195	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775197	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151458	0.94[EUR][1000 genomes]
rs6151459	0.88[EUR][1000 genomes]
rs6151460	0.94[EUR][1000 genomes]
rs6151461	0.94[EUR][1000 genomes]
rs6151462	0.94[EUR][1000 genomes]
rs6151467	0.94[EUR][1000 genomes]
rs6151470	0.94[EUR][1000 genomes]
rs6151472	0.92[EUR][1000 genomes]
rs6151474	0.94[EUR][1000 genomes]
rs6151477	0.94[EUR][1000 genomes]
rs6151483	0.85[EUR][1000 genomes]
rs6151486	0.94[EUR][1000 genomes]
rs6151487	0.85[EUR][1000 genomes]
rs6151501	0.94[EUR][1000 genomes]
rs6151503	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151504	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151506	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151514	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151525	0.86[EUR][1000 genomes]
rs6151528	0.94[EUR][1000 genomes]
rs6151529	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151532	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151533	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151535	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151536	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151542	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151545	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151551	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151553	0.87[EUR][1000 genomes]
rs6151557	0.84[EUR][1000 genomes]
rs6151561	0.86[EUR][1000 genomes]
rs6151565	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151568	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151570	0.86[EUR][1000 genomes]
rs6151571	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151574	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151576	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151580	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151581	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151586	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151588	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151589	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151590	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151592	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62012358	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62015260	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62015289	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494127	0.84[EUR][1000 genomes]
rs6494128	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6494130	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6494131	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494133	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67697180	0.87[EUR][1000 genomes]
rs67820349	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7162964	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7164756	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172270	0.84[EUR][1000 genomes]
rs7178050	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7180408	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182962	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs722163	0.94[EUR][1000 genomes]
rs722164	0.94[EUR][1000 genomes]
rs7497974	0.87[EUR][1000 genomes]
rs7882	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8027679	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033161	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035465	0.80[EUR][1000 genomes]
rs8040114	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8041394	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	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
6	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
rs12441240	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	chr15:59905200-59946200	Weak transcription	Gastric	stomach
2	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
3	chr15:59925000-59943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:59925800-59943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:59926600-59944000	Weak transcription	Fetal Kidney	kidney
7	chr15:59926600-59947600	Weak transcription	Right Ventricle	heart
8	chr15:59926600-59948000	Weak transcription	Brain Angular Gyrus	brain
9	chr15:59927200-59948800	Weak transcription	Aorta	Aorta
10	chr15:59927400-59943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:59928400-59945600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:59929000-59944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:59929000-59947200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:59929200-59947600	Weak transcription	Ovary	ovary
15	chr15:59929600-59945800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr15:59929800-59946400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:59930600-59948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:59932800-59947800	Weak transcription	Colonic Mucosa	Colon
19	chr15:59932800-59948000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:59935200-59943600	Weak transcription	Stomach Mucosa	stomach
21	chr15:59935600-59944200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:59935800-59944200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:59935800-59945000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:59936000-59944200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr15:59936000-59945600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:59936000-59946000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr15:59936000-59948000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:59936200-59946600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:59936400-59946800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:59936400-59946800	Strong transcription	Duodenum Mucosa	Duodenum
31	chr15:59936400-59947000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:59936600-59944000	Strong transcription	Adipose Nuclei	Adipose
33	chr15:59936600-59945000	Strong transcription	NHDF-Ad	bronchial
34	chr15:59936600-59945200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:59936600-59945800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:59936600-59946800	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:59936600-59946800	Strong transcription	Dnd41	blood
38	chr15:59936600-59947000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:59937000-59946200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:59937400-59947600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:59937600-59944000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:59937600-59944000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:59937600-59944000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:59937600-59944000	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:59937600-59944000	Weak transcription	Fetal Brain Male	brain
46	chr15:59937600-59946600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:59937800-59943800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr15:59937800-59944000	Weak transcription	Brain Substantia Nigra	brain
49	chr15:59937800-59944000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:59938200-59943600	Weak transcription	Fetal Intestine Large	intestine

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