Variant report

Variant	rs17086786
Chromosome Location	chr4:57329255-57329256
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57328019-57329668	K562	blood:	n/a	n/a
2	POLR2A	chr4:57329124-57329642	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr4:57327632-57330405	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:57329099-57329664	HL-60	blood:	n/a	n/a
5	POLR2A	chr4:57326457-57334588	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:57329051-57334155	U87	brain:	n/a	n/a
7	POLR2A	chr4:57329113-57329662	GM12891	blood:	n/a	n/a
8	POLR2A	chr4:57329061-57330517	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr4:57328023-57334626	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr4:57328727-57329753	K562	blood:	n/a	n/a
11	POLR2A	chr4:57328174-57331217	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:57329148-57329626	HCT-116	colon:	n/a	n/a
13	POLR2A	chr4:57329197-57334826	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:57329144-57329733	HepG2	liver:	n/a	n/a
15	POLR2A	chr4:57329109-57330469	GM12892	blood:	n/a	n/a
16	POLR2A	chr4:57327841-57334590	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr4:57329166-57330470	GM12892	blood:	n/a	n/a
18	POLR2A	chr4:57329230-57329462	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr4:57328020-57330417	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:57328083-57331197	A549	lung:	n/a	n/a
21	POLR2A	chr4:57321294-57335320	K562	blood:	n/a	n/a
22	POLR2A	chr4:57328117-57329577	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr4:57327796-57331218	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr4:57328291-57334478	K562	blood:	n/a	n/a
25	POLR2A	chr4:57329108-57329727	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:57329078-57330520	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr4:57329100-57330387	GM12892	blood:	n/a	n/a
28	POLR2A	chr4:57328181-57330365	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr4:57328090-57334773	GM12878	blood:	n/a	n/a
30	STAT3	chr4:57329240-57329416	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr4:57329145-57329662	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr4:57326028-57334384	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr4:57328983-57329842	K562	blood:	n/a	n/a
34	POLR2A	chr4:57329076-57330423	GM12891	blood:	n/a	n/a
35	POLR2A	chr4:57328331-57329488	K562	blood:	n/a	n/a
36	POLR2A	chr4:57329138-57331157	K562	blood:	n/a	n/a
37	POLR2A	chr4:57329223-57329577	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr4:57329179-57329659	K562	blood:	n/a	n/a
39	POLR2A	chr4:57329172-57332331	GM12891	blood:	n/a	n/a
40	POLR2A	chr4:57328052-57329655	GM12891	blood:	n/a	n/a
41	PML	chr4:57329088-57329661	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57302068..57304080-chr4:57328689..57330198,2	MCF-7	breast:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPAT-1	chr4:57327536-57333761	NONHSAT096505

No data

Variant related genes	Relation type
SRP72	TF binding region
ENSG00000270109	TF binding region
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10866436	0.81[JPT][hapmap]
rs1401908	0.89[JPT][hapmap]
rs17086746	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17086755	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17086769	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086776	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086844	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086924	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292984	0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs28649329	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34228795	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34543011	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796543	0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4074775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41476944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57439970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58337902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61580407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61732641	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73155895	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73155901	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73157733	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73157739	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73157754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157772	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159992	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73162272	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73167378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73167396	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7437329	0.90[JPT][hapmap]
rs7686452	0.81[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17086786	ARL9	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
2	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
3	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
4	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
5	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
6	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
7	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
10	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
12	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
13	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:57306600-57329400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:57306600-57330200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:57306600-57330400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:57306800-57330200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:57306800-57331000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:57307000-57330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:57307200-57329600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:57307400-57329400	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr4:57307400-57329400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:57307400-57329400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:57307400-57329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:57307400-57329800	Strong transcription	K562	blood
26	chr4:57307400-57330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:57308800-57330000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:57309000-57330600	Weak transcription	Fetal Brain Male	brain
29	chr4:57313800-57329400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:57314000-57330600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:57314600-57329400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:57314600-57330200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:57314600-57330600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:57314600-57330800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:57314800-57329400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr4:57315000-57331800	Weak transcription	Aorta	Aorta
37	chr4:57315200-57329400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:57315600-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:57316000-57330200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:57316600-57330400	Strong transcription	Osteobl	bone
41	chr4:57316800-57330200	Strong transcription	HSMM	muscle
42	chr4:57318600-57329600	Strong transcription	Fetal Intestine Large	intestine
43	chr4:57318600-57329600	Strong transcription	Placenta	Placenta
44	chr4:57318800-57330000	Strong transcription	GM12878-XiMat	blood
45	chr4:57318800-57330400	Strong transcription	Primary T cells from cord blood	blood
46	chr4:57318800-57331600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:57319000-57330400	Strong transcription	A549	lung
48	chr4:57319200-57331600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:57319600-57330800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:57321600-57330600	Weak transcription	Rectal Smooth Muscle	rectum

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