Variant report

Variant	rs999072
Chromosome Location	chr20:23347553-23347554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:23347217-23347634	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:23345662-23352219	GM12878	blood:	n/a	n/a
3	JUN	chr20:23346956-23347598	K562	blood:	n/a	chr20:23347202-23347211 chr20:23347198-23347211
4	USF2	chr20:23347053-23347800	GM12878	blood:	n/a	chr20:23347237-23347248
5	MXI1	chr20:23346992-23347807	GM12878	blood:	n/a	n/a
6	POLR2A	chr20:23347112-23347978	HepG2	liver:	n/a	n/a
7	FOSL2	chr20:23346977-23347597	HepG2	liver:	n/a	chr20:23347202-23347211
8	POLR2A	chr20:23341279-23355011	HepG2	liver:	n/a	n/a
9	NFATC1	chr20:23347115-23347787	GM12878	blood:	n/a	n/a
10	POLR2A	chr20:23341069-23355530	K562	blood:	n/a	n/a
11	EP300	chr20:23347020-23347825	GM12878	blood:	n/a	n/a
12	CUX1	chr20:23347293-23347711	GM12878	blood:	n/a	n/a
13	POLR2A	chr20:23347245-23348258	A549	lung:	n/a	n/a
14	GATA1	chr20:23346949-23347908	PBDE	blood:	n/a	chr20:23347313-23347320 chr20:23347491-23347504
15	CHD2	chr20:23346980-23347558	GM12878	blood:	n/a	n/a
16	POLR2A	chr20:23346314-23348823	GM12891	blood:	n/a	n/a
17	GATA1	chr20:23346928-23348123	K562	blood:	n/a	chr20:23347313-23347320 chr20:23347491-23347504
18	EP300	chr20:23347070-23347661	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23345633..23349899-chr20:23400647..23404181,5	K562	blood:
2	chr20:23345633..23349899-chr20:23400854..23404181,4	K562	blood:

Variant related genes	Relation type
GZF1	TF binding region
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1003417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281430	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2405231	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2424533	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424538	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2424547	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424553	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]
rs6048777	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048797	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6076065	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6083105	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6083106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs743021	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs761723	0.81[CEU][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs999072	NAPB	cis	Artery Tibial	GTEx
rs999072	NAPB	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23342400-23352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23344000-23347600	Enhancers	Primary T cells fromperipheralblood	blood
3	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:23344400-23347800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:23344400-23349200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:23344400-23350200	Weak transcription	Fetal Kidney	kidney
7	chr20:23344600-23354200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:23344800-23347800	Genic enhancers	Brain Inferior Temporal Lobe	brain
9	chr20:23344800-23347800	Strong transcription	A549	lung
10	chr20:23344800-23348800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
11	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr20:23345000-23348200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
13	chr20:23345000-23349600	Genic enhancers	HepG2	liver
14	chr20:23345000-23361800	Strong transcription	Fetal Thymus	thymus
15	chr20:23345000-23362000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr20:23345200-23348200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr20:23345400-23347600	Strong transcription	HSMMtube	muscle
19	chr20:23345800-23347600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr20:23345800-23348400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr20:23346000-23347800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:23346000-23347800	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr20:23346000-23348200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr20:23346200-23347600	Genic enhancers	Adipose Nuclei	Adipose
25	chr20:23346200-23347600	Genic enhancers	Stomach Smooth Muscle	stomach
26	chr20:23346200-23347800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr20:23346200-23347800	Genic enhancers	Brain Cingulate Gyrus	brain
28	chr20:23346200-23348000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr20:23346200-23348400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
30	chr20:23346200-23348800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr20:23346200-23349400	Genic enhancers	HMEC	breast
32	chr20:23346400-23347600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr20:23346400-23347600	Genic enhancers	Primary T cells from cord blood	blood
34	chr20:23346400-23347600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr20:23346400-23347800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr20:23346400-23347800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr20:23346400-23347800	Enhancers	Primary B cells from cord blood	blood
38	chr20:23346400-23347800	Genic enhancers	Primary hematopoietic stem cells	blood
39	chr20:23346400-23347800	Enhancers	Duodenum Mucosa	Duodenum
40	chr20:23346400-23348000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr20:23346400-23348000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr20:23346400-23348000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr20:23346400-23348000	Genic enhancers	Brain Anterior Caudate	brain
44	chr20:23346400-23348000	Genic enhancers	Brain Germinal Matrix	brain
45	chr20:23346400-23348600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr20:23346400-23348600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr20:23346400-23348800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr20:23346400-23348800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr20:23346400-23349600	Genic enhancers	K562	blood
50	chr20:23346400-23349800	Weak transcription	H9 Cell Line	embryonic stem cell

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