Variant report

Variant	rs1520026
Chromosome Location	chr4:57300557-57300558
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	ZNF263	chr4:57299174-57300723	HEK293-T-REx	kidney:	n/a	n/a
2	CUX1	chr4:57300400-57300764	GM12878	blood:	n/a	n/a
3	RCOR1	chr4:57300494-57302764	K562	blood:	n/a	n/a
4	TBP	chr4:57300179-57301315	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr4:57300047-57300686	Hela-S3	cervix:	n/a	n/a
6	RFX5	chr4:57300370-57301162	Hela-S3	cervix:	n/a	chr4:57300987-57301004
7	MXI1	chr4:57300482-57302815	Hela-S3	cervix:	n/a	n/a
8	UBTF	chr4:57299970-57302790	K562	blood:	n/a	n/a
9	STAT3	chr4:57300347-57300673	MCF10A-Er-Src	breast:	n/a	n/a
10	CUX1	chr4:57300347-57301148	K562	blood:	n/a	n/a
11	CHD1	chr4:57300152-57300693	H1-hESC	embryonic stem cell:	n/a	n/a
12	JUND	chr4:57300219-57302743	K562	blood:	n/a	chr4:57301262-57301271 chr4:57302581-57302590
13	CEBPB	chr4:57300070-57300573	K562	blood:	n/a	n/a
14	FOXA1	chr4:57300165-57300611	HepG2	liver:	n/a	n/a
15	POLR2A	chr4:57300296-57303752	H1-hESC	embryonic stem cell:	n/a	n/a
16	EP300	chr4:57300526-57300655	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr4:57300307-57302602	K562	blood:	n/a	n/a
18	MAX	chr4:57300318-57300641	NB4	blood:	n/a	n/a
19	MYC	chr4:57300333-57302866	MCF10A-Er-Src	breast:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
20	HCFC1	chr4:57300121-57302986	Hela-S3	cervix:	n/a	n/a
21	MYC	chr4:57300550-57303840	K562	blood:	n/a	chr4:57302554-57302564 chr4:57301487-57301497 chr4:57302555-57302564 chr4:57301655-57301666 chr4:57301657-57301664 chr4:57302623-57302632 chr4:57302554-57302565 chr4:57301656-57301665 chr4:57301655-57301665 chr4:57302555-57302564 chr4:57302556-57302563 chr4:57301957-57301964
22	EP300	chr4:57300420-57301216	K562	blood:	n/a	n/a
23	STAT3	chr4:57300436-57300591	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:57300337-57303731	MCF10A-Er-Src	breast:	n/a	n/a
25	SIN3A	chr4:57300533-57303708	H1-hESC	embryonic stem cell:	n/a	chr4:57301877-57301888
26	MXI1	chr4:57300180-57304365	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
2	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
3	chr4:57298757..57303397-chr4:57395270..57398462,7	K562	blood:
4	chr4:57275711..57277429-chr4:57298915..57301727,2	K562	blood:
5	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:
6	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
7	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
8	chr4:57275040..57277242-chr4:57300118..57301937,2	MCF-7	breast:
9	chr4:57299474..57303800-chr4:57395386..57399526,7	K562	blood:
10	chr4:57299951..57301849-chr4:57773604..57776000,3	K562	blood:
11	chr4:56813951..56816639-chr4:57299941..57302593,2	K562	blood:
12	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
13	chr4:57251780..57255283-chr4:57300557..57304376,5	MCF-7	breast:

Variant related genes	Relation type
PAICS	TF binding region
ENSG00000157426	Chromatin interaction
ENSG00000268171	Chromatin interaction
ENSG00000270109	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000174799	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1060472	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11133443	0.80[TSI][hapmap]
rs12498340	0.83[TSI][hapmap]
rs12501334	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12501502	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12503412	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12504291	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12510712	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12511770	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1401907	0.86[JPT][hapmap]
rs1474179	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1520030	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17086696	0.83[TSI][hapmap]
rs1967559	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2049087	0.88[MEX][hapmap]
rs2271923	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28866881	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3796541	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796548	0.80[TSI][hapmap]
rs4346704	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4493603	1.00[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4864583	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5010012	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs56392224	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58151706	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66810706	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6819534	0.88[MEX][hapmap]
rs6820314	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6821301	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6829250	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6832797	0.86[EUR][1000 genomes]
rs6834696	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6836118	0.80[TSI][hapmap]
rs6846895	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7664841	1.00[CEU][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7671868	0.91[JPT][hapmap]
rs8340	0.83[TSI][hapmap]
rs9996593	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1520026	AASDH	cis	parietal	SCAN
rs1520026	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs1520026	AASDH	cis	cerebellum	SCAN
rs1520026	SRP72	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:57295000-57305000	Active TSS	GM12878-XiMat	blood
4	chr4:57298400-57305600	Active TSS	Hela-S3	cervix
5	chr4:57299200-57300600	Flanking Active TSS	Dnd41	blood
6	chr4:57299200-57300800	Enhancers	Primary B cells from peripheral blood	blood
7	chr4:57299200-57300800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr4:57299200-57300800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr4:57299200-57302600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:57299200-57304000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:57299200-57304200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr4:57299200-57304400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:57299200-57304400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr4:57299200-57304800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:57299200-57305000	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr4:57299200-57305800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr4:57299200-57305800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:57299200-57305800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr4:57299400-57300800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:57299400-57301000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:57299400-57301200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:57299400-57301400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:57299400-57304200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr4:57299400-57304200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:57299400-57304400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:57299400-57304800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:57299400-57305000	Active TSS	K562	blood
28	chr4:57299600-57300600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr4:57299600-57300800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr4:57299600-57300800	Flanking Active TSS	HUVEC	blood vessel
31	chr4:57299600-57301000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr4:57299600-57304400	Active TSS	A549	lung
33	chr4:57299800-57300600	Enhancers	Primary T cells from cord blood	blood
34	chr4:57299800-57301200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:57299800-57301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:57299800-57303000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr4:57299800-57304400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:57299800-57304400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:57299800-57304400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:57299800-57304800	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr4:57299800-57305600	Active TSS	HepG2	liver
42	chr4:57300000-57300600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr4:57300000-57300800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr4:57300000-57300800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr4:57300000-57304000	Active TSS	HSMM	muscle
46	chr4:57300000-57304400	Active TSS	Ovary	ovary
47	chr4:57300200-57300600	Enhancers	Colonic Mucosa	Colon
48	chr4:57300200-57300600	Enhancers	Colon Smooth Muscle	Colon
49	chr4:57300200-57300600	Active TSS	Fetal Brain Female	brain
50	chr4:57300200-57300600	Flanking Active TSS	Fetal Kidney	kidney

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