Variant report

Variant	rs12350531
Chromosome Location	chr9:116356373-116356374
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:197)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:197 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr9:116356043-116356445	GM12878	blood:	n/a	n/a
2	TAF1	chr9:116355987-116356800	A549	lung:	n/a	n/a
3	MAX	chr9:116355916-116356550	A549	lung:	n/a	chr9:116356274-116356284
4	POLR2A	chr9:116356067-116356762	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:116355865-116356756	GM18951	blood:	n/a	n/a
6	EP300	chr9:116356011-116356425	SK-N-SH_RA	brain:	n/a	n/a
7	FOSL2	chr9:116356116-116356713	SK-N-SH	brain:	n/a	n/a
8	FOS	chr9:116356231-116356557	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr9:116355854-116363729	IMR90	lung:	n/a	n/a
10	TAF1	chr9:116356198-116356636	SK-N-SH	brain:	n/a	n/a
11	SIN3AK20	chr9:116356012-116356648	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr9:116355952-116356747	H1-hESC	embryonic stem cell:	n/a	n/a
13	FOS	chr9:116356223-116356502	MCF10A-Er-Src	breast:	n/a	n/a
14	TAF1	chr9:116356294-116356615	HepG2	liver:	n/a	n/a
15	RAD21	chr9:116356002-116356791	SK-N-SH_RA	brain:	n/a	n/a
16	CHD1	chr9:116355774-116358399	IMR90	lung:	n/a	n/a
17	POLR2A	chr9:116356273-116356595	HepG2	liver:	n/a	n/a
18	RAD21	chr9:116355872-116357284	IMR90	lung:	n/a	chr9:116357082-116357095
19	USF2	chr9:116356172-116356468	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF384	chr9:116355951-116356469	GM12878	blood:	n/a	n/a
21	FOSL2	chr9:116355931-116356732	A549	lung:	n/a	n/a
22	RAD21	chr9:116355825-116356678	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr9:116356350-116356463	K562	blood:	n/a	n/a
24	POLR2A	chr9:116355972-116357585	GM12878	blood:	n/a	n/a
25	CTBP2	chr9:116355814-116356676	H1-hESC	embryonic stem cell:	n/a	n/a
26	JUND	chr9:116356004-116356799	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr9:116356274-116356536	HepG2	liver:	n/a	n/a
28	POLR2A	chr9:116356313-116356583	HepG2	liver:	n/a	n/a
29	POLR2A	chr9:116356233-116356567	HCT-116	colon:	n/a	n/a
30	POLR2A	chr9:116356163-116356685	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr9:116356152-116356595	A549	lung:	n/a	n/a
32	TAF1	chr9:116355942-116356691	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr9:116356335-116356537	GM12878	blood:	n/a	n/a
34	TEAD4	chr9:116355966-116356693	SK-N-SH	brain:	n/a	n/a
35	MAX	chr9:116355976-116356694	H1-hESC	embryonic stem cell:	n/a	chr9:116356274-116356284
36	FOSL2	chr9:116356157-116356582	HepG2	liver:	n/a	n/a
37	CTCF	chr9:116356300-116356450	SK-N-SH_RA	brain:	n/a	n/a
38	SP1	chr9:116355866-116356608	H1-hESC	embryonic stem cell:	n/a	n/a
39	HEY1	chr9:116356167-116356602	HepG2	liver:	n/a	n/a
40	REST	chr9:116356243-116356630	SK-N-SH	brain:	n/a	n/a
41	IRF1	chr9:116356163-116356397	K562	blood:	n/a	n/a
42	POLR2A	chr9:116356024-116356685	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr9:116356198-116356674	SK-N-SH	brain:	n/a	n/a
44	ELF1	chr9:116355960-116356387	GM12878	blood:	n/a	n/a
45	CTCF	chr9:116356320-116356470	HCPEpiC	choroid plexus:	n/a	n/a
46	EGR1	chr9:116356035-116356389	H1-hESC	embryonic stem cell:	n/a	n/a
47	SP4	chr9:116356027-116356612	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr9:116355824-116356891	SK-N-SH	brain:	n/a	n/a
49	GTF2F1	chr9:116356081-116356549	H1-hESC	embryonic stem cell:	n/a	n/a
50	FOS	chr9:116356229-116356502	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116036733..116038262-chr9:116353878..116356485,2	MCF-7	breast:

No data

Variant related genes	Relation type
RGS3	TF binding region
ENSG00000237073	TF binding region
ENSG00000176386	Chromatin interaction
ENSG00000136875	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1051013	0.80[EUR][1000 genomes]
rs10739393	0.85[JPT][hapmap]
rs10817493	0.84[EUR][1000 genomes]
rs12685417	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12686023	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs17187621	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4979253	0.92[JPT][hapmap]
rs4979261	0.85[JPT][hapmap]
rs518636	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs567743	0.84[EUR][1000 genomes]
rs568557	0.87[EUR][1000 genomes]
rs58449392	0.81[ASN][1000 genomes]
rs72763856	0.93[ASN][1000 genomes]
rs818714	0.85[JPT][hapmap]
rs944343	0.80[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116343200-116358800	Weak transcription	Hela-S3	cervix
2	chr9:116346600-116356800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:116348000-116361600	Weak transcription	Dnd41	blood
4	chr9:116348200-116356400	Weak transcription	Aorta	Aorta
5	chr9:116352200-116357400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:116352400-116357000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:116352400-116357600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:116352400-116358000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr9:116352400-116363200	Weak transcription	Thymus	Thymus
10	chr9:116352600-116357000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr9:116353200-116361000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr9:116353200-116361400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:116353400-116356400	Enhancers	Placenta	Placenta
14	chr9:116353400-116361400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:116353800-116360400	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:116354200-116356400	Weak transcription	Gastric	stomach
17	chr9:116354200-116356800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:116354800-116356400	Enhancers	Spleen	Spleen
19	chr9:116354800-116357000	Weak transcription	Primary T cells from cord blood	blood
20	chr9:116355200-116356400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:116355200-116356400	Flanking Active TSS	GM12878-XiMat	blood
22	chr9:116355200-116357200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:116355400-116356400	Enhancers	Fetal Thymus	thymus
24	chr9:116355400-116356400	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr9:116355400-116356600	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr9:116355400-116356600	Enhancers	Primary B cells from peripheral blood	blood
27	chr9:116355600-116357000	Enhancers	Primary B cells from cord blood	blood
28	chr9:116355800-116356400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:116355800-116356400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:116355800-116356400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:116355800-116356400	Genic enhancers	Colonic Mucosa	Colon
32	chr9:116355800-116356400	Enhancers	Fetal Intestine Large	intestine
33	chr9:116355800-116356400	Enhancers	Left Ventricle	heart
34	chr9:116355800-116356400	Enhancers	Lung	lung
35	chr9:116355800-116356400	Enhancers	Pancreas	Pancrea
36	chr9:116355800-116356400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr9:116355800-116356400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr9:116355800-116356400	Enhancers	NHEK	skin
39	chr9:116355800-116356600	Flanking Active TSS	Fetal Brain Female	brain
40	chr9:116355800-116357000	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr9:116355800-116357000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr9:116355800-116357200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr9:116355800-116357200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:116355800-116357400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr9:116355800-116357400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr9:116355800-116357400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:116355800-116357400	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr9:116355800-116357400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr9:116355800-116357400	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr9:116355800-116357600	Enhancers	Fetal Brain Male	brain

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