Variant report

Variant	rs4815198
Chromosome Location	chr20:23343491-23343492
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	TAF1	chr20:23342048-23343519	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr20:23341477-23343789	MCF-7	breast:	n/a	n/a
3	POLR2A	chr20:23341578-23343854	HepG2	liver:	n/a	n/a
4	CTCF	chr20:23343420-23343570	AG10803	skin:	n/a	n/a
5	REST	chr20:23341663-23343881	H1-neurons	neurons:	n/a	chr20:23342152-23342165 chr20:23342981-23342994 chr20:23343187-23343196 chr20:23343180-23343193 chr20:23342841-23342850 chr20:23342155-23342168
6	SIN3AK20	chr20:23341981-23343589	MCF-7	breast:	n/a	n/a
7	HMGN3	chr20:23342065-23343517	K562	blood:	n/a	n/a
8	SMARCB1	chr20:23341980-23343501	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr20:23342075-23343607	GM12878	blood:	n/a	n/a
10	MAX	chr20:23341652-23343723	HepG2	liver:	n/a	chr20:23342507-23342516 chr20:23342510-23342518 chr20:23342189-23342199
11	CTCF	chr20:23343440-23343590	NHDF-neo	bronchial:	n/a	n/a
12	POLR2A	chr20:23341738-23343553	GM12892	blood:	n/a	n/a
13	POLR2A	chr20:23341746-23344311	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr20:23341369-23343586	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr20:23341671-23343555	HUVEC	blood vessel:	n/a	n/a
16	SIN3AK20	chr20:23342066-23343536	HepG2	liver:	n/a	n/a
17	POLR2A	chr20:23342983-23344157	GM12891	blood:	n/a	n/a
18	EBF1	chr20:23343243-23343614	GM12878	blood:	n/a	n/a
19	CHD2	chr20:23341819-23343505	HepG2	liver:	n/a	n/a
20	POLR2A	chr20:23341932-23343538	HEK293	kidney:	n/a	n/a
21	MAZ	chr20:23341574-23344142	IMR90	lung:	n/a	chr20:23342507-23342516 chr20:23342510-23342518 chr20:23342189-23342199
22	POLR2A	chr20:23341670-23343501	GM18526	blood:	n/a	n/a
23	MAZ	chr20:23343357-23343744	K562	blood:	n/a	n/a
24	POLR2A	chr20:23341795-23343824	H1-neurons	neurons:	n/a	n/a
25	MXI1	chr20:23341170-23344193	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr20:23341923-23343644	GM12892	blood:	n/a	n/a
27	CHD1	chr20:23341243-23344756	IMR90	lung:	n/a	n/a
28	CEBPB	chr20:23343288-23343623	Hela-S3	cervix:	n/a	chr20:23343474-23343485
29	POLR2A	chr20:23341682-23344387	GM12878	blood:	n/a	n/a
30	CREB1	chr20:23341744-23344099	HepG2	liver:	n/a	n/a
31	CEBPB	chr20:23343301-23343647	IMR90	lung:	n/a	chr20:23343474-23343485
32	CTCF	chr20:23343401-23343898	GM12878	blood:	n/a	n/a
33	SIN3A	chr20:23341822-23343936	H1-hESC	embryonic stem cell:	n/a	chr20:23343183-23343196 chr20:23343128-23343137 chr20:23342679-23342690 chr20:23342508-23342517 chr20:23342837-23342850 chr20:23342185-23342196 chr20:23342506-23342515
34	POLR2A	chr20:23342990-23344042	GM12878	blood:	n/a	n/a
35	POLR2A	chr20:23342005-23343720	H1-neurons	neurons:	n/a	n/a
36	MTA3	chr20:23342985-23344167	GM12878	blood:	n/a	n/a
37	POLR2A	chr20:23341279-23355011	HepG2	liver:	n/a	n/a
38	POLR2A	chr20:23341222-23343551	GM12878	blood:	n/a	n/a
39	SIN3AK20	chr20:23343081-23343557	H1-hESC	embryonic stem cell:	n/a	n/a
40	SIN3A	chr20:23341985-23343502	GM12878	blood:	n/a	chr20:23343183-23343196 chr20:23343128-23343137 chr20:23342679-23342690 chr20:23342508-23342517 chr20:23342837-23342850 chr20:23342185-23342196 chr20:23342506-23342515
41	POLR2A	chr20:23343064-23343578	GM12891	blood:	n/a	n/a
42	POLR2A	chr20:23341931-23343604	HL-60	blood:	n/a	n/a
43	POLR2A	chr20:23342024-23343500	A549	lung:	n/a	n/a
44	POLR2A	chr20:23341737-23343591	GM12878	blood:	n/a	n/a
45	POLR2A	chr20:23341714-23343572	GM18951	blood:	n/a	n/a
46	POLR2A	chr20:23341552-23343561	NB4	blood:	n/a	n/a
47	POLR2A	chr20:23341168-23344354	Raji	blood:	n/a	n/a
48	POLR2A	chr20:23341730-23344290	GM19193	blood:	n/a	n/a
49	TAF1	chr20:23342111-23343604	H1-neurons	neurons:	n/a	n/a
50	CEBPB	chr20:23343314-23343599	HepG2	liver:	n/a	chr20:23343474-23343485

No.	Distal block	Cell Line	Cell type
1	chr20:23112532..23115241-chr20:23342774..23344532,2	K562	blood:
2	chr14:20922188..20924523-chr20:23341669..23343744,2	MCF-7	breast:
3	chr2:38978307..38979883-chr20:23342389..23345213,2	MCF-7	breast:
4	chr20:23340976..23344072-chr20:23400128..23403114,5	K562	blood:
5	chr20:23342672..23344892-chr20:23400555..23402881,3	MCF-7	breast:
6	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:
7	chr20:23337918..23344174-chr20:23400107..23404916,9	MCF-7	breast:
8	chr15:71407056..71408775-chr20:23342043..23343755,2	MCF-7	breast:
9	chr20:23343192..23343938-chr20:23587080..23587607,2	MCF-7	breast:
10	chr20:23338809..23345308-chr20:23399768..23403114,12	K562	blood:

Variant related genes	Relation type
ENSG00000232645	TF binding region
GZF1	TF binding region
ENSG00000233746	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000092094	Chromatin interaction
ENSG00000101439	Chromatin interaction
ENSG00000100823	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000225362	Chromatin interaction
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1016628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12349	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1419007	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2024746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2180139	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2236023	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2243448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2253834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2281431	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2295239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2424527	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2424542	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424555	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4142246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048750	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048760	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6048784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6076055	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6083114	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137933	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs761723	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs999068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3338336	chr20:23341577-23344125	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4815198	NAPB	cis	Skin Sun Exposed Lower leg	GTEx
rs4815198	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	chr20:23341200-23343600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr20:23341400-23343800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr20:23341600-23343600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr20:23341600-23343800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr20:23341600-23343800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr20:23341800-23343600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:23341800-23343600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:23341800-23343600	Active TSS	Ovary	ovary
9	chr20:23341800-23343600	Active TSS	Psoas Muscle	Psoas
10	chr20:23341800-23343800	Active TSS	Lung	lung
11	chr20:23342000-23343600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:23342000-23343600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr20:23342000-23343600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr20:23342000-23343600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr20:23342000-23343600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:23342000-23343600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:23342000-23343600	Active TSS	Brain Angular Gyrus	brain
18	chr20:23342000-23343600	Active TSS	Fetal Intestine Small	intestine
19	chr20:23342000-23343600	Active TSS	Gastric	stomach
20	chr20:23342000-23343600	Active TSS	Pancreas	Pancrea
21	chr20:23342000-23343600	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr20:23342000-23343600	Active TSS	Small Intestine	intestine
23	chr20:23342000-23343600	Active TSS	A549	lung
24	chr20:23342000-23343600	Active TSS	Hela-S3	cervix
25	chr20:23342000-23343600	Bivalent/Poised TSS	HepG2	liver
26	chr20:23342000-23343600	Active TSS	NHDF-Ad	bronchial
27	chr20:23342000-23343800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr20:23342000-23343800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:23342000-23343800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:23342000-23343800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr20:23342000-23343800	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr20:23342000-23343800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr20:23342000-23343800	Active TSS	Aorta	Aorta
34	chr20:23342000-23343800	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr20:23342000-23343800	Active TSS	Fetal Kidney	kidney
36	chr20:23342000-23343800	Active TSS	Left Ventricle	heart
37	chr20:23342000-23343800	Active TSS	Right Atrium	heart
38	chr20:23342000-23343800	Active TSS	HSMMtube	muscle
39	chr20:23342000-23343800	Active TSS	K562	blood
40	chr20:23342000-23344200	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr20:23342000-23344200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr20:23342200-23343600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:23342200-23343600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:23342200-23343600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
45	chr20:23342200-23343600	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr20:23342200-23343600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr20:23342200-23343600	Active TSS	HSMM	muscle
48	chr20:23342200-23343600	Active TSS	Osteobl	bone
49	chr20:23342200-23343800	Active TSS	GM12878-XiMat	blood
50	chr20:23342400-23343800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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