Variant report

Variant	rs6151459
Chromosome Location	chr15:59977668-59977669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59975789..59979387-chr15:59979488..59982275,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140299	Chromatin interaction
ENSG00000259238	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1002181	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10152209	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10152373	0.81[AFR][1000 genomes]
rs10152414	0.87[EUR][1000 genomes]
rs10152415	0.87[EUR][1000 genomes]
rs10162629	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1046053	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10519039	0.80[AFR][1000 genomes]
rs1057059	0.89[EUR][1000 genomes]
rs11071465	0.88[EUR][1000 genomes]
rs11071468	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11071469	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1135148	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634067	0.86[EUR][1000 genomes]
rs11853610	0.85[EUR][1000 genomes]
rs11854063	0.88[EUR][1000 genomes]
rs12440020	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12441240	0.88[EUR][1000 genomes]
rs12443242	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12593480	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12708458	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12708459	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902582	0.87[EUR][1000 genomes]
rs12903647	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906392	0.86[EUR][1000 genomes]
rs12907554	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910451	0.81[ASN][1000 genomes]
rs12912652	0.82[EUR][1000 genomes]
rs1531638	0.81[EUR][1000 genomes]
rs1531639	0.81[EUR][1000 genomes]
rs1552031	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17236804	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1871499	0.81[EUR][1000 genomes]
rs1871500	0.88[EUR][1000 genomes]
rs1871503	0.83[EUR][1000 genomes]
rs2306355	0.89[EUR][1000 genomes]
rs2306357	0.81[ASN][1000 genomes]
rs2306358	0.81[ASN][1000 genomes]
rs2307272	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2307273	0.81[EUR][1000 genomes]
rs2307275	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28671744	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2899649	0.82[EUR][1000 genomes]
rs3087328	0.81[ASN][1000 genomes]
rs34797071	0.86[EUR][1000 genomes]
rs34894301	0.84[EUR][1000 genomes]
rs3784389	0.85[EUR][1000 genomes]
rs3825870	0.82[EUR][1000 genomes]
rs4270113	0.81[EUR][1000 genomes]
rs4533213	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774340	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4774341	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775191	0.83[EUR][1000 genomes]
rs4775195	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4775197	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56141740	0.81[ASN][1000 genomes]
rs6151440	0.82[ASN][1000 genomes]
rs6151442	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6151444	0.83[ASN][1000 genomes]
rs6151445	0.83[ASN][1000 genomes]
rs6151446	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6151447	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6151448	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6151449	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6151450	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6151451	0.82[ASN][1000 genomes]
rs6151458	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151460	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151461	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151462	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151464	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151467	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151470	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151472	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151474	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151477	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151483	0.84[EUR][1000 genomes]
rs6151486	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151487	0.84[EUR][1000 genomes]
rs6151491	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6151494	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6151496	0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6151501	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151503	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6151504	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6151506	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6151514	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151525	0.83[EUR][1000 genomes]
rs6151528	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6151529	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151532	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151533	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151535	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151536	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151542	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151545	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6151551	0.82[EUR][1000 genomes]
rs6151553	0.82[EUR][1000 genomes]
rs6151561	0.81[EUR][1000 genomes]
rs6151565	0.81[EUR][1000 genomes]
rs6151568	0.89[EUR][1000 genomes]
rs6151570	0.81[EUR][1000 genomes]
rs6151571	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6151574	0.89[EUR][1000 genomes]
rs6151576	0.81[EUR][1000 genomes]
rs6151580	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6151581	0.86[EUR][1000 genomes]
rs6151586	0.89[EUR][1000 genomes]
rs6151588	0.89[EUR][1000 genomes]
rs6151589	0.88[EUR][1000 genomes]
rs6151590	0.89[EUR][1000 genomes]
rs6151592	0.81[EUR][1000 genomes]
rs62012358	0.81[EUR][1000 genomes]
rs62015289	0.90[EUR][1000 genomes]
rs6494128	0.81[EUR][1000 genomes]
rs6494130	0.81[EUR][1000 genomes]
rs6494131	0.87[EUR][1000 genomes]
rs6494133	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6494138	0.81[ASN][1000 genomes]
rs67820349	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7162964	0.80[EUR][1000 genomes]
rs7164756	0.87[EUR][1000 genomes]
rs7178050	0.81[EUR][1000 genomes]
rs7180408	0.87[EUR][1000 genomes]
rs7182962	0.85[EUR][1000 genomes]
rs722163	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs722164	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs728037	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs728038	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs74017838	0.80[AFR][1000 genomes]
rs7497974	0.82[EUR][1000 genomes]
rs754642	0.81[ASN][1000 genomes]
rs754643	0.81[ASN][1000 genomes]
rs755605	0.81[ASN][1000 genomes]
rs7882	0.81[EUR][1000 genomes]
rs8033161	0.89[EUR][1000 genomes]
rs8040114	0.81[EUR][1000 genomes]
rs8041394	0.88[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
rs6151459	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	chr15:59951400-59978800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:59952000-59977800	Strong transcription	Hela-S3	cervix
6	chr15:59952400-59978600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:59962000-59979400	Weak transcription	Fetal Heart	heart
8	chr15:59965000-59980200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:59968200-59979600	Weak transcription	Fetal Brain Male	brain
10	chr15:59969600-59978400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:59969600-59980000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:59970200-59978400	Weak transcription	Psoas Muscle	Psoas
13	chr15:59970600-59979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:59970800-59979800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:59973200-59979600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:59973400-59980000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:59973600-59977800	Weak transcription	HSMM	muscle
18	chr15:59973600-59980000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:59973600-59980000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:59973600-59980000	Weak transcription	Esophagus	oesophagus
21	chr15:59973800-59977800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:59973800-59977800	Weak transcription	Brain Anterior Caudate	brain
23	chr15:59973800-59978200	Weak transcription	Fetal Kidney	kidney
24	chr15:59973800-59978400	Weak transcription	Brain Germinal Matrix	brain
25	chr15:59973800-59979600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:59973800-59979600	Weak transcription	Brain Angular Gyrus	brain
27	chr15:59974000-59978200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:59974000-59978400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:59974000-59979600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:59974000-59979800	Weak transcription	Fetal Brain Female	brain
31	chr15:59974200-59978000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:59974200-59978200	Weak transcription	Fetal Lung	lung
33	chr15:59974200-59978400	Weak transcription	NH-A	brain
34	chr15:59974400-59978200	Weak transcription	HMEC	breast
35	chr15:59974400-59978400	Weak transcription	Aorta	Aorta
36	chr15:59974400-59978400	Weak transcription	Right Ventricle	heart
37	chr15:59974400-59979600	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:59974400-59979600	Weak transcription	Ovary	ovary
39	chr15:59974400-59979600	Weak transcription	Spleen	Spleen
40	chr15:59974400-59980000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:59974400-59980000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:59974400-59980000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:59974400-59980000	Weak transcription	Lung	lung
44	chr15:59974600-59978400	Weak transcription	Thymus	Thymus
45	chr15:59974600-59979800	Weak transcription	Fetal Stomach	stomach
46	chr15:59974600-59980000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:59974800-59977800	Weak transcription	Osteobl	bone
48	chr15:59974800-59978200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:59974800-59978400	Weak transcription	Fetal Intestine Large	intestine
50	chr15:59974800-59979600	Weak transcription	Stomach Smooth Muscle	stomach

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