Variant report

Variant	rs1718862
Chromosome Location	chr4:57889332-57889333
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	BCL3	chr4:57889206-57889844	A549	lung:	n/a	n/a
2	STAT3	chr4:57889223-57889824	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr4:57889235-57889705	IMR90	lung:	n/a	n/a
4	E2F4	chr4:57889267-57889514	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr4:57889308-57889686	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr4:57888609-57890165	HUVEC	blood vessel:	n/a	n/a
7	FOS	chr4:57889228-57889779	MCF10A-Er-Src	breast:	n/a	chr4:57889425-57889436 chr4:57889378-57889389
8	FOS	chr4:57889193-57889729	MCF10A-Er-Src	breast:	n/a	chr4:57889425-57889436 chr4:57889378-57889389
9	POLR2A	chr4:57888893-57889767	A549	lung:	n/a	n/a
10	RCOR1	chr4:57889056-57890000	IMR90	lung:	n/a	n/a
11	POLR2A	chr4:57889127-57889783	U87	brain:	n/a	n/a
12	POLR2A	chr4:57888987-57889798	IMR90	lung:	n/a	n/a
13	FOS	chr4:57889188-57889648	HUVEC	blood vessel:	n/a	chr4:57889425-57889436 chr4:57889378-57889389
14	POLR2A	chr4:57889059-57889920	HUVEC	blood vessel:	n/a	n/a
15	STAT3	chr4:57889228-57889760	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr4:57889283-57889690	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr4:57889197-57889721	U87	brain:	n/a	n/a
18	MAFK	chr4:57889151-57889667	IMR90	lung:	n/a	n/a
19	FOS	chr4:57889233-57889746	MCF10A-Er-Src	breast:	n/a	chr4:57889425-57889436 chr4:57889378-57889389
20	GATA2	chr4:57889288-57889783	HUVEC	blood vessel:	n/a	chr4:57889292-57889302
21	RAD21	chr4:57889236-57889666	IMR90	lung:	n/a	n/a
22	STAT3	chr4:57889261-57889818	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr4:57889264-57889665	MCF10A-Er-Src	breast:	n/a	chr4:57889425-57889436 chr4:57889378-57889389
24	POLR2A	chr4:57889204-57889860	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57843255..57845274-chr4:57888366..57890332,2	K562	blood:
2	chr4:57843255..57844990-chr4:57888825..57890332,2	K562	blood:

Variant related genes	Relation type
POLR2B	TF binding region
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11934764	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1277279	0.88[AMR][1000 genomes]
rs1277281	0.89[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1277282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277285	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277286	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277289	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1277302	0.84[AFR][1000 genomes]
rs1277307	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1277309	1.00[ASN][1000 genomes]
rs1277310	1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1299618	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1708764	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1713949	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1713951	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718838	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1718866	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718885	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2687239	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs7683519	0.87[YRI][hapmap]
rs7687211	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1718862	ARL9	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:57848600-57900000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:57849000-57900000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
5	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
7	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr4:57851200-57897200	Strong transcription	Fetal Intestine Large	intestine
9	chr4:57851400-57894800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:57851600-57899400	Strong transcription	Placenta	Placenta
11	chr4:57851800-57899400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:57851800-57899400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:57851800-57899400	Strong transcription	Liver	Liver
14	chr4:57851800-57899600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:57852000-57892200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:57852000-57894800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:57852000-57898200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr4:57852200-57899000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:57852200-57899400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:57852600-57899400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr4:57856000-57899400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:57856800-57900000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr4:57858200-57899800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:57859000-57898000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr4:57859400-57898600	Strong transcription	Dnd41	blood
28	chr4:57859600-57897800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:57860200-57898800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:57860600-57892800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:57861400-57895000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr4:57862200-57891600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:57862200-57899400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:57862200-57900000	Strong transcription	Fetal Muscle Leg	muscle
35	chr4:57863400-57907800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:57863600-57892000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:57866600-57894000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:57870400-57894400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr4:57870400-57899800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:57870600-57897200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:57870600-57899000	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:57870800-57897200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:57871000-57899600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr4:57871800-57893000	Strong transcription	GM12878-XiMat	blood
45	chr4:57871800-57897800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:57872800-57892600	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr4:57873000-57894000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:57879400-57899800	Strong transcription	Fetal Kidney	kidney
49	chr4:57880000-57890800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:57880000-57894400	Weak transcription	Stomach Mucosa	stomach

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