Variant report

Variant	rs4845360
Chromosome Location	chr1:153966660-153966661
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:84)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:84 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153965956-153967991	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:153966136-153966700	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:153965118-153967275	HepG2	liver:	n/a	n/a
4	PML	chr1:153966467-153966868	K562	blood:	n/a	n/a
5	POLR2A	chr1:153962781-153968523	GM12892	blood:	n/a	n/a
6	ATF2	chr1:153966191-153966781	H1-hESC	embryonic stem cell:	n/a	n/a
7	PML	chr1:153966017-153966972	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:153962895-153968418	K562	blood:	n/a	n/a
9	POLR2A	chr1:153965873-153968470	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:153966143-153966991	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:153966058-153966668	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr1:153962997-153968485	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:153965956-153966850	U87	brain:	n/a	n/a
14	POLR2A	chr1:153966056-153967215	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:153966076-153967256	K562	blood:	n/a	n/a
16	POLR2A	chr1:153965885-153968440	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:153966275-153966718	HL-60	blood:	n/a	n/a
18	POLR2A	chr1:153965580-153967871	K562	blood:	n/a	n/a
19	POLR2A	chr1:153965052-153967793	GM18505	blood:	n/a	n/a
20	POLR2A	chr1:153965057-153968372	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:153966162-153966668	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:153964943-153967891	K562	blood:	n/a	n/a
23	POLR2A	chr1:153964976-153968525	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr1:153966636-153966699	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:153966060-153967131	MCF-7	breast:	n/a	n/a
26	POLR2A	chr1:153966240-153966844	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr1:153965183-153968489	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:153965066-153967273	GM12878	blood:	n/a	n/a
29	MTA3	chr1:153965939-153967318	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:153966592-153966933	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr1:153962877-153968982	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr1:153965957-153967254	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:153966067-153967267	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr1:153966357-153966813	K562	blood:	n/a	n/a
35	POLR2A	chr1:153965880-153967410	U87	brain:	n/a	n/a
36	POLR2A	chr1:153966087-153966750	HCT-116	colon:	n/a	n/a
37	POLR2A	chr1:153962912-153967853	GM12892	blood:	n/a	n/a
38	POLR2A	chr1:153962884-153969250	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr1:153964793-153967747	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:153962902-153967332	GM12892	blood:	n/a	n/a
41	POLR2A	chr1:153962875-153969575	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr1:153962850-153967268	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:153966073-153968235	Hela-S3	cervix:	n/a	n/a
44	HEY1	chr1:153965998-153966852	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:153966101-153966875	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr1:153965069-153969409	A549	lung:	n/a	n/a
47	HEY1	chr1:153965994-153967011	HepG2	liver:	n/a	n/a
48	POLR2A	chr1:153964987-153967906	GM12891	blood:	n/a	n/a
49	POLR2A	chr1:153965942-153966883	HepG2	liver:	n/a	n/a
50	JUND	chr1:153966126-153966673	A549	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153966124..153968225-chr1:154141847..154143966,3	K562	blood:
2	chr1:153745179..153749280-chr1:153961747..153968478,7	MCF-7	breast:
3	chr1:153961938..153967162-chr1:154189861..154195978,9	K562	blood:
4	chr1:153964844..153966669-chr1:154089731..154091606,2	MCF-7	breast:
5	chr1:153966171..153967933-chr1:153980339..153982819,2	MCF-7	breast:
6	chr1:153962189..153967020-chr1:154149779..154153923,7	MCF-7	breast:
7	chr1:153966341..153968649-chr1:154153580..154156511,2	K562	blood:
8	chr1:153965322..153967162-chr1:154193447..154195978,2	K562	blood:
9	chr1:153629459..153632821-chr1:153961630..153966753,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231416	TF binding region
ENSG00000143612	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143553	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10127484	1.00[CHB][hapmap]
rs10908578	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs11264573	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs11264736	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11264972	1.00[JPT][hapmap]
rs12142733	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap]
rs1591902	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1832582	1.00[JPT][hapmap]
rs2252508	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs2790686	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs2790690	0.85[YRI][hapmap]
rs2841108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs3001365	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[ASN][1000 genomes]
rs4845586	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6661009	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6671362	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7414227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs7521047	0.81[GIH][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs7522030	1.00[CHD][hapmap];0.93[GIH][hapmap]
rs7537213	0.81[GIH][hapmap];0.85[YRI][hapmap]
rs9427318	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4845360	CTAG2	trans	parietal	SCAN
rs4845360	CREB3L4	cis	Nerve Tibial	GTEx
rs4845360	FLG	cis	parietal	SCAN
rs4845360	HAX1	cis	cerebellum	SCAN
rs4845360	SLC27A3	cis	cerebellum	SCAN
rs4845360	PSMD4	cis	parietal	SCAN
rs4845360	GATAD2B	cis	cerebellum	SCAN
rs4845360	SLC25A44	cis	parietal	SCAN
rs4845360	GBA	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153963400-153966800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr1:153964000-153969800	Weak transcription	Esophagus	oesophagus
3	chr1:153964200-153966800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:153964200-153969000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:153964400-153967600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:153964400-153968400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr1:153964600-153966800	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr1:153964600-153966800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:153964600-153968400	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr1:153964600-153968400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:153964600-153968400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:153964600-153968400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:153964600-153968400	Strong transcription	Thymus	Thymus
14	chr1:153964600-153969000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:153964800-153966800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:153964800-153966800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:153964800-153967800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:153964800-153968400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:153964800-153968400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr1:153965000-153968400	Strong transcription	Aorta	Aorta
21	chr1:153965200-153967800	Strong transcription	Gastric	stomach
22	chr1:153965200-153968600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:153965400-153966800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:153965400-153966800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:153965400-153966800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:153965400-153966800	Strong transcription	Colonic Mucosa	Colon
27	chr1:153965400-153966800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:153965400-153966800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:153965400-153966800	Strong transcription	HSMM	muscle
30	chr1:153965400-153966800	Strong transcription	HSMMtube	muscle
31	chr1:153965400-153967200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:153965400-153967200	Strong transcription	Fetal Lung	lung
33	chr1:153965400-153967400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:153965400-153967600	Strong transcription	Pancreas	Pancrea
35	chr1:153965400-153967800	Weak transcription	Right Ventricle	heart
36	chr1:153965400-153968000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:153965400-153968200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:153965400-153968400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:153965400-153968400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:153965400-153968400	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:153965400-153968400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:153965400-153968800	Strong transcription	Fetal Brain Female	brain
43	chr1:153965400-153972800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:153965400-153973000	Weak transcription	Stomach Mucosa	stomach
45	chr1:153965600-153966800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:153965600-153966800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:153965600-153966800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr1:153965600-153966800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:153965600-153966800	Strong transcription	Psoas Muscle	Psoas
50	chr1:153965600-153966800	Strong transcription	NH-A	brain

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