Variant report

Variant	rs12909005
Chromosome Location	chr15:59935347-59935348
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	chr15:59934768..59938897-chr15:59945804..59950909,4	K562	blood:

Variant related genes	Relation type
ENSG00000140307	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1002181	0.84[EUR][1000 genomes]
rs10152209	0.87[EUR][1000 genomes]
rs10152414	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10152415	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10152509	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10162629	0.85[EUR][1000 genomes]
rs1046053	0.86[EUR][1000 genomes]
rs1057059	0.87[EUR][1000 genomes]
rs11071465	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11071468	0.85[EUR][1000 genomes]
rs11071469	0.85[EUR][1000 genomes]
rs1135148	0.82[EUR][1000 genomes]
rs11634067	0.87[EUR][1000 genomes]
rs11637071	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637359	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11853610	0.87[EUR][1000 genomes]
rs11854063	0.85[EUR][1000 genomes]
rs12441240	0.88[EUR][1000 genomes]
rs12593480	0.85[EUR][1000 genomes]
rs12708458	0.88[EUR][1000 genomes]
rs12708459	0.88[EUR][1000 genomes]
rs12902582	0.86[EUR][1000 genomes]
rs12902774	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903647	0.82[EUR][1000 genomes]
rs12906392	0.87[EUR][1000 genomes]
rs12907554	0.84[EUR][1000 genomes]
rs12907641	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912652	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1479885	0.80[EUR][1000 genomes]
rs1531638	0.84[EUR][1000 genomes]
rs1531639	0.84[EUR][1000 genomes]
rs1552031	0.84[EUR][1000 genomes]
rs1871499	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1871500	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1871503	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1979422	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2101019	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170062	0.93[EUR][1000 genomes]
rs2306354	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306355	0.87[EUR][1000 genomes]
rs2307272	0.84[EUR][1000 genomes]
rs2307273	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2307275	0.83[EUR][1000 genomes]
rs2414638	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28671744	0.86[EUR][1000 genomes]
rs2899649	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34797071	0.87[EUR][1000 genomes]
rs34894301	0.85[EUR][1000 genomes]
rs3825870	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4270113	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4533213	0.83[EUR][1000 genomes]
rs4774340	0.88[EUR][1000 genomes]
rs4774341	0.87[EUR][1000 genomes]
rs4775191	0.86[EUR][1000 genomes]
rs4775195	0.86[EUR][1000 genomes]
rs4775197	0.84[EUR][1000 genomes]
rs6151458	0.83[EUR][1000 genomes]
rs6151460	0.83[EUR][1000 genomes]
rs6151461	0.83[EUR][1000 genomes]
rs6151462	0.83[EUR][1000 genomes]
rs6151467	0.83[EUR][1000 genomes]
rs6151470	0.83[EUR][1000 genomes]
rs6151472	0.82[EUR][1000 genomes]
rs6151474	0.83[EUR][1000 genomes]
rs6151477	0.83[EUR][1000 genomes]
rs6151483	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6151486	0.83[EUR][1000 genomes]
rs6151487	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6151501	0.82[EUR][1000 genomes]
rs6151503	0.84[EUR][1000 genomes]
rs6151504	0.84[EUR][1000 genomes]
rs6151506	0.84[EUR][1000 genomes]
rs6151510	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6151514	0.83[EUR][1000 genomes]
rs6151525	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151528	0.83[EUR][1000 genomes]
rs6151529	0.83[EUR][1000 genomes]
rs6151532	0.83[EUR][1000 genomes]
rs6151533	0.84[EUR][1000 genomes]
rs6151535	0.85[EUR][1000 genomes]
rs6151536	0.85[EUR][1000 genomes]
rs6151542	0.85[EUR][1000 genomes]
rs6151545	0.85[EUR][1000 genomes]
rs6151551	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151553	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6151557	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151561	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151565	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6151568	0.84[EUR][1000 genomes]
rs6151570	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151571	0.84[EUR][1000 genomes]
rs6151574	0.84[EUR][1000 genomes]
rs6151576	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151580	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6151581	0.83[EUR][1000 genomes]
rs6151586	0.87[EUR][1000 genomes]
rs6151588	0.87[EUR][1000 genomes]
rs6151589	0.85[EUR][1000 genomes]
rs6151590	0.87[EUR][1000 genomes]
rs6151592	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62012358	0.84[EUR][1000 genomes]
rs62015260	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62015289	0.85[EUR][1000 genomes]
rs6494127	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6494128	0.84[EUR][1000 genomes]
rs6494130	0.84[EUR][1000 genomes]
rs6494131	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6494133	0.86[EUR][1000 genomes]
rs67697180	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67820349	0.84[EUR][1000 genomes]
rs7164756	0.85[EUR][1000 genomes]
rs7172270	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178050	0.84[EUR][1000 genomes]
rs7180408	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7182962	0.86[EUR][1000 genomes]
rs722163	0.83[EUR][1000 genomes]
rs722164	0.83[EUR][1000 genomes]
rs7497974	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7882	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033161	0.87[EUR][1000 genomes]
rs8035465	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040114	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8041394	0.81[AMR][1000 genomes];0.87[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
rs12909005	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59905200-59946200	Weak transcription	Gastric	stomach
2	chr15:59914800-59937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
4	chr15:59925000-59936800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:59925000-59936800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:59925000-59943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:59925400-59937200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:59925600-59936600	Weak transcription	NHLF	lung
9	chr15:59925600-59937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:59925800-59936600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:59925800-59943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:59926200-59936800	Weak transcription	Fetal Brain Male	brain
14	chr15:59926200-59937000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:59926400-59935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:59926400-59936600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:59926600-59936600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:59926600-59944000	Weak transcription	Fetal Kidney	kidney
19	chr15:59926600-59947600	Weak transcription	Right Ventricle	heart
20	chr15:59926600-59948000	Weak transcription	Brain Angular Gyrus	brain
21	chr15:59927000-59937000	Weak transcription	Lung	lung
22	chr15:59927200-59936600	Weak transcription	HMEC	breast
23	chr15:59927200-59948800	Weak transcription	Aorta	Aorta
24	chr15:59927400-59943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:59927600-59936200	Weak transcription	Pancreas	Pancrea
26	chr15:59927800-59942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:59928400-59936600	Weak transcription	Brain Anterior Caudate	brain
28	chr15:59928400-59940200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:59928400-59945600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:59928600-59936400	Weak transcription	HSMMtube	muscle
31	chr15:59928800-59937400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:59928800-59942000	Weak transcription	Fetal Heart	heart
33	chr15:59929000-59936600	Weak transcription	Brain Substantia Nigra	brain
34	chr15:59929000-59936800	Weak transcription	Esophagus	oesophagus
35	chr15:59929000-59942200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:59929000-59944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:59929000-59947200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:59929200-59936200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:59929200-59941400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:59929200-59947600	Weak transcription	Ovary	ovary
41	chr15:59929600-59942400	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:59929600-59945800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:59929800-59936800	Weak transcription	Spleen	Spleen
44	chr15:59929800-59940200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:59929800-59946400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:59930000-59937800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:59930400-59936000	Weak transcription	Fetal Brain Female	brain
48	chr15:59930600-59936200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:59930600-59936600	Weak transcription	Thymus	Thymus
50	chr15:59930600-59936600	Weak transcription	NHEK	skin

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