Variant report

Variant	rs1520030
Chromosome Location	chr4:57255624-57255625
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57255490-57256053	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:57255619-57256930	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:57255534-57255960	HepG2	liver:	n/a	n/a
4	ARID3A	chr4:57255586-57256089	K562	blood:	n/a	n/a
5	POLR2A	chr4:57255571-57257314	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr4:57252843-57257309	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:57253046-57257192	GM12891	blood:	n/a	n/a
8	POLR2A	chr4:57255602-57258077	GM12892	blood:	n/a	n/a
9	POLR2A	chr4:57255548-57256472	PBDE	blood:	n/a	n/a
10	GATA1	chr4:57253159-57256476	PBDE	blood:	n/a	chr4:57253785-57253794 chr4:57255968-57255978 chr4:57256193-57256204
11	IRF1	chr4:57255557-57256485	K562	blood:	n/a	n/a
12	POLR2A	chr4:57255594-57256472	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr4:57255214-57257232	Hela-S3	cervix:	n/a	n/a
14	PML	chr4:57255502-57256262	K562	blood:	n/a	n/a
15	POLR2A	chr4:57255613-57256530	PFSK-1	brain:	n/a	n/a
16	TEAD4	chr4:57255603-57256298	K562	blood:	n/a	n/a
17	PML	chr4:57255617-57256183	K562	blood:	n/a	n/a
18	MXI1	chr4:57255581-57256245	K562	blood:	n/a	n/a
19	TAL1	chr4:57255545-57256599	K562	blood:	n/a	chr4:57255971-57255989
20	TBL1XR1	chr4:57255535-57256144	K562	blood:	n/a	n/a
21	POLR2A	chr4:57253107-57259459	K562	blood:	n/a	n/a
22	STAT5A	chr4:57255611-57256202	K562	blood:	n/a	chr4:57256063-57256070
23	POLR2A	chr4:57255247-57256478	K562	blood:	n/a	n/a
24	NR2F2	chr4:57255452-57256202	K562	blood:	n/a	n/a
25	TEAD4	chr4:57255621-57256212	K562	blood:	n/a	n/a
26	EP300	chr4:57255514-57256064	GM12878	blood:	n/a	chr4:57255823-57255833

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
2	chr4:57254546..57256143-chr4:57396737..57398873,2	K562	blood:
3	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
4	chr4:57252113..57256281-chr4:57265528..57268374,5	MCF-7	breast:
5	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
6	chr4:57255304..57257966-chr4:57332773..57334646,2	MCF-7	breast:
7	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAICS-3	chr4:57253640-57259528	NONHSAT096500

No data

Variant related genes	Relation type
AASDH	TF binding region
ENSG00000174780	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000249693	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10434444	0.91[YRI][hapmap]
rs10434445	0.84[EUR][1000 genomes]
rs1060472	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12498340	0.81[YRI][hapmap]
rs12501334	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12501502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503412	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12504291	1.00[CEU][hapmap]
rs12510712	0.80[EUR][1000 genomes]
rs1401907	0.91[JPT][hapmap]
rs1474179	0.82[EUR][1000 genomes]
rs1520026	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	0.81[YRI][hapmap]
rs1967559	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1983378	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2271923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28866881	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3796541	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822001	0.81[CEU][hapmap]
rs4493603	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864579	0.82[YRI][hapmap]
rs4864583	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4865092	0.80[AFR][1000 genomes]
rs5010012	0.92[CEU][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs56392224	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58151706	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66810706	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820314	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6821301	1.00[CEU][hapmap]
rs6829250	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6832797	0.84[EUR][1000 genomes]
rs6834696	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6846895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664841	1.00[CEU][hapmap]
rs7671868	0.95[JPT][hapmap]
rs8340	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1520030	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs1520030	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254400-57256400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:57254400-57268400	Weak transcription	Lung	lung
4	chr4:57254400-57273600	Weak transcription	Pancreas	Pancrea
5	chr4:57254600-57255800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr4:57254600-57264000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:57254600-57271600	Weak transcription	Ovary	ovary
8	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
9	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:57254800-57256000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr4:57254800-57256000	Weak transcription	Gastric	stomach
12	chr4:57254800-57256200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr4:57254800-57260800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:57254800-57261800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:57254800-57262000	Weak transcription	Placenta	Placenta
16	chr4:57254800-57264000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:57254800-57264000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:57254800-57271600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:57254800-57273200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
24	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
25	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr4:57255000-57255800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr4:57255000-57255800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:57255000-57255800	Enhancers	Hela-S3	cervix
29	chr4:57255000-57256000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr4:57255000-57256200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr4:57255000-57256200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr4:57255000-57257800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:57255000-57260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:57255000-57261200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:57255000-57262200	Weak transcription	A549	lung
36	chr4:57255000-57264400	Weak transcription	Brain Germinal Matrix	brain
37	chr4:57255000-57264800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr4:57255000-57265600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:57255000-57266000	Weak transcription	Primary B cells from cord blood	blood
40	chr4:57255000-57266200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:57255000-57266200	Weak transcription	NH-A	brain
42	chr4:57255000-57266400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:57255000-57266400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:57255000-57266600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:57255000-57266600	Weak transcription	HSMM	muscle
46	chr4:57255000-57266800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:57255000-57269200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr4:57255000-57271400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:57255200-57255800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:57255200-57255800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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