Variant report

Variant	rs6151451
Chromosome Location	chr15:59979920-59979921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr15:59979737-59981942	A549	lung:	n/a	n/a
2	POLR2A	chr15:59979315-59982513	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:59979906-59980475	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:59979869-59982333	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr15:59979865-59982169	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:59979863-59982314	Hela-S3	cervix:	n/a	n/a
7	GATA1	chr15:59979887-59982469	PBDE	blood:	n/a	n/a
8	SIN3A	chr15:59979857-59980415	GM12878	blood:	n/a	n/a
9	WRNIP1	chr15:59979747-59980303	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:59979863-59980251	HepG2	liver:	n/a	n/a
11	TBL1XR1	chr15:59979883-59981049	K562	blood:	n/a	n/a
12	JUN	chr15:59979681-59982479	K562	blood:	n/a	n/a
13	POLR2A	chr15:59979847-59982081	K562	blood:	n/a	n/a
14	SPI1	chr15:59979907-59980410	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:59979872-59982471	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr15:59979846-59982515	PBDE	blood:	n/a	n/a
17	ELK4	chr15:59979891-59981786	Hela-S3	cervix:	n/a	chr15:59980292-59980300 chr15:59980289-59980300 chr15:59980291-59980300
18	POLR2A	chr15:59979741-59982196	IMR90	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59979537..59981515-chr15:60770595..60772119,2	K562	blood:
2	chr15:59979548..59984505-chr15:60688391..60691990,7	K562	blood:
3	chr15:59979537..59982042-chr15:60770595..60772312,3	K562	blood:
4	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
5	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
6	chr15:59979503..59981285-chr3:183330477..183331977,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259238	TF binding region
ENSG00000243584	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000140307	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000182718	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1002181	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10152209	0.81[AMR][1000 genomes]
rs10152431	0.82[AFR][1000 genomes]
rs10152791	0.83[AFR][1000 genomes]
rs10162629	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1046053	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11071468	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11071469	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11071471	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11634157	0.82[EUR][1000 genomes]
rs12438078	0.91[EUR][1000 genomes]
rs12439645	0.80[EUR][1000 genomes]
rs12440020	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12442896	0.87[EUR][1000 genomes]
rs12443242	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12443297	0.89[EUR][1000 genomes]
rs12593480	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12903647	0.83[ASN][1000 genomes]
rs12904505	0.81[EUR][1000 genomes]
rs12907554	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12910451	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13379702	0.82[AFR][1000 genomes]
rs13380147	0.84[AFR][1000 genomes]
rs1552031	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16941645	0.86[AFR][1000 genomes]
rs16941648	0.83[AFR][1000 genomes]
rs17236804	0.85[ASN][1000 genomes]
rs17236867	0.84[EUR][1000 genomes]
rs1871504	0.90[EUR][1000 genomes]
rs2306357	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306358	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2307272	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2307275	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3087328	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3843695	0.83[EUR][1000 genomes]
rs3848119	0.85[EUR][1000 genomes]
rs3936513	0.84[EUR][1000 genomes]
rs4533213	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4774340	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4774341	0.81[AMR][1000 genomes]
rs4775195	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4775200	0.82[EUR][1000 genomes]
rs56141740	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151440	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151441	0.90[EUR][1000 genomes]
rs6151442	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151444	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151445	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151446	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151447	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151448	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151449	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151450	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151458	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151459	0.82[ASN][1000 genomes]
rs6151460	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151461	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151462	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151467	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151470	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6151472	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151474	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6151477	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6151486	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6151491	0.85[ASN][1000 genomes]
rs6151494	0.85[ASN][1000 genomes]
rs6151496	0.85[ASN][1000 genomes]
rs6151501	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151503	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151504	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151506	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151514	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151528	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6151529	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151532	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151533	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151535	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151536	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151542	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6151545	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6494133	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6494138	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494139	0.89[EUR][1000 genomes]
rs6494140	0.81[EUR][1000 genomes]
rs67712565	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs67820349	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7162645	0.81[EUR][1000 genomes]
rs7173534	0.89[EUR][1000 genomes]
rs7173827	0.89[EUR][1000 genomes]
rs7178211	0.89[EUR][1000 genomes]
rs722163	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs722164	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72625734	0.83[AFR][1000 genomes]
rs728037	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs728038	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs754641	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs754642	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754643	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs755605	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8025415	0.83[AFR][1000 genomes]
rs8026680	0.83[AFR][1000 genomes]
rs8027353	0.81[AFR][1000 genomes]
rs8027389	0.81[AFR][1000 genomes]
rs8027415	0.81[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6151451	GTF2A2	cis	Whole Blood	GTEx
rs6151451	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	chr15:59965000-59980200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:59969600-59980000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:59973400-59980000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:59973600-59980000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:59973600-59980000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:59973600-59980000	Weak transcription	Esophagus	oesophagus
8	chr15:59974400-59980000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:59974400-59980000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:59974400-59980000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:59974400-59980000	Weak transcription	Lung	lung
12	chr15:59974600-59980000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:59976400-59980400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:59977000-59980400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr15:59977200-59981000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:59977400-59980000	Enhancers	Gastric	stomach
17	chr15:59977400-59980000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr15:59977600-59980000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr15:59977600-59980200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:59977800-59980600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr15:59977800-59980800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:59977800-59981000	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr15:59978000-59980200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr15:59978200-59981000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr15:59978400-59980600	Enhancers	Small Intestine	intestine
26	chr15:59978800-59980000	Enhancers	Placenta	Placenta
27	chr15:59979000-59980000	Weak transcription	Brain Germinal Matrix	brain
28	chr15:59979000-59980000	Enhancers	Fetal Muscle Trunk	muscle
29	chr15:59979200-59980000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:59979200-59980000	Weak transcription	Aorta	Aorta
31	chr15:59979400-59980000	Enhancers	Fetal Heart	heart
32	chr15:59979400-59980200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:59979400-59980200	Flanking Active TSS	HepG2	liver
34	chr15:59979400-59980400	Flanking Active TSS	HUVEC	blood vessel
35	chr15:59979400-59980600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr15:59979400-59980600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr15:59979600-59980000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:59979600-59980000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr15:59979600-59980000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:59979600-59980000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:59979600-59980000	Enhancers	Brain Angular Gyrus	brain
42	chr15:59979600-59980000	Enhancers	Fetal Kidney	kidney
43	chr15:59979600-59980000	Enhancers	Ovary	ovary
44	chr15:59979600-59980200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:59979600-59980200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:59979600-59980200	Flanking Active TSS	Psoas Muscle	Psoas
47	chr15:59979600-59980200	Transcr. at gene 5' and 3'	HSMM	muscle
48	chr15:59979600-59980400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:59979600-59980400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:59979600-59980400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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