Variant report

Variant	rs62015260
Chromosome Location	chr15:59926657-59926658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59923114..59927076-chr15:59929959..59933582,4	K562	blood:
2	chr15:59917418..59919231-chr15:59924681..59927270,2	K562	blood:
3	chr15:59923114..59927076-chr15:59930243..59933582,3	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1002181	0.82[EUR][1000 genomes]
rs10152209	0.86[EUR][1000 genomes]
rs10152414	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10152415	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10152509	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10162629	0.83[EUR][1000 genomes]
rs1046053	0.84[EUR][1000 genomes]
rs1057059	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11071465	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11071468	0.83[EUR][1000 genomes]
rs11071469	0.83[EUR][1000 genomes]
rs11630029	0.83[AFR][1000 genomes]
rs11634067	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11637071	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11637359	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11853610	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11854063	0.83[EUR][1000 genomes]
rs12441240	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12593480	0.83[EUR][1000 genomes]
rs12708458	0.86[EUR][1000 genomes]
rs12708459	0.86[EUR][1000 genomes]
rs12902582	0.84[EUR][1000 genomes]
rs12902774	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906392	0.85[EUR][1000 genomes]
rs12907554	0.82[EUR][1000 genomes]
rs12907641	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12909005	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12912652	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1531638	0.86[EUR][1000 genomes]
rs1531639	0.87[EUR][1000 genomes]
rs1552031	0.82[EUR][1000 genomes]
rs1871499	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1871500	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1871503	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1979422	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2101019	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2170062	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2306354	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306355	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2307272	0.82[EUR][1000 genomes]
rs2307273	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2307275	0.81[EUR][1000 genomes]
rs2414638	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28671744	0.85[EUR][1000 genomes]
rs2899649	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34797071	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34894301	0.84[EUR][1000 genomes]
rs3825870	0.88[EUR][1000 genomes]
rs4270113	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4533213	0.81[EUR][1000 genomes]
rs4774340	0.87[EUR][1000 genomes]
rs4774341	0.86[EUR][1000 genomes]
rs4775191	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4775195	0.84[EUR][1000 genomes]
rs4775197	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6151458	0.81[EUR][1000 genomes]
rs6151460	0.81[EUR][1000 genomes]
rs6151461	0.81[EUR][1000 genomes]
rs6151462	0.81[EUR][1000 genomes]
rs6151467	0.81[EUR][1000 genomes]
rs6151470	0.81[EUR][1000 genomes]
rs6151474	0.81[EUR][1000 genomes]
rs6151477	0.81[EUR][1000 genomes]
rs6151483	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151486	0.81[EUR][1000 genomes]
rs6151487	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151501	0.80[EUR][1000 genomes]
rs6151503	0.82[EUR][1000 genomes]
rs6151504	0.82[EUR][1000 genomes]
rs6151506	0.82[EUR][1000 genomes]
rs6151510	0.86[EUR][1000 genomes]
rs6151514	0.81[EUR][1000 genomes]
rs6151525	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151528	0.81[EUR][1000 genomes]
rs6151529	0.81[EUR][1000 genomes]
rs6151532	0.81[EUR][1000 genomes]
rs6151533	0.82[EUR][1000 genomes]
rs6151535	0.83[EUR][1000 genomes]
rs6151536	0.83[EUR][1000 genomes]
rs6151542	0.83[EUR][1000 genomes]
rs6151545	0.83[EUR][1000 genomes]
rs6151551	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6151553	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6151557	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6151561	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151565	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151568	0.82[EUR][1000 genomes]
rs6151570	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151571	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6151574	0.82[EUR][1000 genomes]
rs6151576	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151580	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6151581	0.81[EUR][1000 genomes]
rs6151586	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151588	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151589	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6151590	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151592	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62012358	0.87[EUR][1000 genomes]
rs62015289	0.83[EUR][1000 genomes]
rs6494127	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6494128	0.86[EUR][1000 genomes]
rs6494130	0.86[EUR][1000 genomes]
rs6494131	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6494133	0.84[EUR][1000 genomes]
rs67697180	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67820349	0.82[EUR][1000 genomes]
rs7164756	0.84[EUR][1000 genomes]
rs7172270	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178050	0.87[EUR][1000 genomes]
rs7180408	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7182962	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs722163	0.81[EUR][1000 genomes]
rs722164	0.81[EUR][1000 genomes]
rs7497974	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7882	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8033161	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8035465	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8040114	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8041394	0.81[AMR][1000 genomes];0.86[EUR][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
rs62015260	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59905200-59931600	Weak transcription	Fetal Stomach	stomach
2	chr15:59905200-59946200	Weak transcription	Gastric	stomach
3	chr15:59909000-59930200	Weak transcription	Fetal Intestine Large	intestine
4	chr15:59911400-59929800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:59912000-59932600	Weak transcription	Colonic Mucosa	Colon
6	chr15:59912200-59928400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:59912200-59935000	Weak transcription	Fetal Intestine Small	intestine
8	chr15:59914800-59937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:59917800-59927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:59917800-59930200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:59919800-59928200	Weak transcription	HSMMtube	muscle
12	chr15:59920600-59928600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
14	chr15:59922200-59929800	Weak transcription	GM12878-XiMat	blood
15	chr15:59922600-59928000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:59923000-59930200	Weak transcription	Osteobl	bone
17	chr15:59924600-59928000	Weak transcription	Fetal Muscle Leg	muscle
18	chr15:59925000-59927400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:59925000-59928200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:59925000-59929800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:59925000-59930200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:59925000-59936800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:59925000-59936800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:59925000-59943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:59925200-59927600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:59925200-59929000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:59925200-59930200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:59925400-59927600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:59925400-59930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:59925400-59930200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:59925400-59930200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:59925400-59937200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:59925600-59928200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:59925600-59928400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:59925600-59931000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:59925600-59936600	Weak transcription	NHLF	lung
37	chr15:59925600-59937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:59925800-59927600	Weak transcription	A549	lung
40	chr15:59925800-59928200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:59925800-59928400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:59925800-59930200	Weak transcription	Brain Germinal Matrix	brain
43	chr15:59925800-59930600	Weak transcription	K562	blood
44	chr15:59925800-59936600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:59925800-59943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:59926000-59928400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:59926000-59928400	Weak transcription	Ovary	ovary
48	chr15:59926000-59928600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:59926000-59928600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr15:59926000-59929800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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