Variant report

Variant	rs1003417
Chromosome Location	chr20:23348007-23348008
allele	A/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	chr20:23345662-23352219	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:23341279-23355011	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:23347641-23348012	HepG2	liver:	n/a	n/a
4	POLR2A	chr20:23341069-23355530	K562	blood:	n/a	n/a
5	POLR2A	chr20:23347245-23348258	A549	lung:	n/a	n/a
6	POLR2A	chr20:23347688-23348101	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr20:23346314-23348823	GM12891	blood:	n/a	n/a
8	GATA1	chr20:23346928-23348123	K562	blood:	n/a	chr20:23347313-23347320 chr20:23347491-23347504

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: 1 )

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

rs_ID	r²[population]
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];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424538	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2424553	1.00[CEU][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]
rs999072	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]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1003417	NAPB	cis	Artery Tibial	GTEx

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	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr20:23344400-23349200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr20:23344400-23350200	Weak transcription	Fetal Kidney	kidney
5	chr20:23344600-23354200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:23344800-23348800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
7	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr20:23345000-23348200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
9	chr20:23345000-23349600	Genic enhancers	HepG2	liver
10	chr20:23345000-23361800	Strong transcription	Fetal Thymus	thymus
11	chr20:23345000-23362000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr20:23345200-23348200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr20:23345800-23348400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr20:23346000-23348200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr20:23346200-23348400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
17	chr20:23346200-23348800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr20:23346200-23349400	Genic enhancers	HMEC	breast
19	chr20:23346400-23348600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr20:23346400-23348600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr20:23346400-23348800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr20:23346400-23348800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
23	chr20:23346400-23349600	Genic enhancers	K562	blood
24	chr20:23346400-23349800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr20:23346400-23350000	Weak transcription	Aorta	Aorta
26	chr20:23346600-23348200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr20:23346600-23348200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr20:23346600-23348200	Enhancers	Psoas Muscle	Psoas
29	chr20:23346600-23348200	Enhancers	Stomach Mucosa	stomach
30	chr20:23346600-23348400	Enhancers	Colon Smooth Muscle	Colon
31	chr20:23346600-23348600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr20:23346600-23348600	Enhancers	Right Ventricle	heart
33	chr20:23346600-23348800	Genic enhancers	Brain Angular Gyrus	brain
34	chr20:23346600-23349200	Enhancers	Brain Hippocampus Middle	brain
35	chr20:23346600-23349400	Enhancers	Liver	Liver
36	chr20:23346600-23349600	Genic enhancers	NHDF-Ad	bronchial
37	chr20:23346600-23349800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:23346600-23363200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr20:23346800-23348200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr20:23346800-23348200	Enhancers	Brain Substantia Nigra	brain
41	chr20:23346800-23348400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr20:23346800-23348800	Genic enhancers	NH-A	brain
43	chr20:23346800-23349400	Weak transcription	Fetal Intestine Large	intestine
44	chr20:23346800-23349400	Weak transcription	Thymus	Thymus
45	chr20:23346800-23349600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr20:23346800-23349800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr20:23346800-23349800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr20:23346800-23349800	Weak transcription	Gastric	stomach
49	chr20:23346800-23349800	Weak transcription	Ovary	ovary
50	chr20:23346800-23349800	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links