Variant report

Variant	rs45572636
Chromosome Location	chr9:104295378-104295379
allele	A/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	MYC	chr9:104295345-104296561	K562	blood:	n/a	n/a
2	REST	chr9:104295267-104296803	H1-neurons	neurons:	n/a	chr9:104296111-104296124
3	POLR2A	chr9:104295331-104296644	U87	brain:	n/a	n/a
4	JUND	chr9:104295370-104296682	K562	blood:	n/a	chr9:104296123-104296132
5	HCFC1	chr9:104295364-104296873	Hela-S3	cervix:	n/a	n/a
6	GABPA	chr9:104295228-104296903	MCF-7	breast:	n/a	chr9:104295974-104295988
7	POLR2A	chr9:104295331-104296638	U87	brain:	n/a	n/a
8	SMC3	chr9:104295334-104295483	GM12878	blood:	n/a	n/a
9	MXI1	chr9:104295239-104296952	SK-N-SH	brain:	n/a	chr9:104295988-104296003
10	GABPA	chr9:104295272-104296802	A549	lung:	n/a	chr9:104295974-104295988
11	BRCA1	chr9:104295333-104296540	Hela-S3	cervix:	n/a	chr9:104295834-104295841
12	NFYA	chr9:104295194-104296118	GM12878	blood:	n/a	chr9:104295786-104295804 chr9:104295434-104295444

Variant related genes	Relation type
RNF20	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10521057	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1113384	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1124148	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12683273	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12684621	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12684773	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12685862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12686025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16920438	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16920479	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16920483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16920504	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1929484	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2150737	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743465	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57053192	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59111885	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59837044	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72743378	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72743387	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72743390	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72743392	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72743394	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72743396	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72743397	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72745315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72745318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7867496	0.85[ASN][1000 genomes]
rs7873168	0.85[ASN][1000 genomes]

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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104289800-104295400	Weak transcription	NHEK	skin
2	chr9:104290200-104295400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:104291000-104295400	Weak transcription	Brain Hippocampus Middle	brain
4	chr9:104291400-104295400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:104291600-104295800	Weak transcription	Small Intestine	intestine
6	chr9:104292400-104295400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:104294800-104295400	Enhancers	Duodenum Mucosa	Duodenum
8	chr9:104295000-104295400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:104295000-104295400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr9:104295000-104295400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr9:104295000-104295400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:104295000-104295400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:104295000-104296200	Active TSS	Fetal Lung	lung
14	chr9:104295200-104295400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:104295200-104295400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr9:104295200-104295400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:104295200-104295400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:104295200-104295400	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr9:104295200-104295400	Active TSS	Primary B cells from cord blood	blood
20	chr9:104295200-104295400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr9:104295200-104295400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:104295200-104295400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr9:104295200-104295400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr9:104295200-104295400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr9:104295200-104295400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:104295200-104295400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:104295200-104295400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr9:104295200-104295400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:104295200-104295400	Active TSS	Adipose Nuclei	Adipose
30	chr9:104295200-104295400	Enhancers	Liver	Liver
31	chr9:104295200-104295400	Enhancers	Brain Angular Gyrus	brain
32	chr9:104295200-104295400	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr9:104295200-104295400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr9:104295200-104295400	Active TSS	Fetal Brain Male	brain
35	chr9:104295200-104295400	Enhancers	Placenta	Placenta
36	chr9:104295200-104295400	Enhancers	Stomach Mucosa	stomach
37	chr9:104295200-104295400	Flanking Active TSS	A549	lung
38	chr9:104295200-104295400	Enhancers	Dnd41	blood
39	chr9:104295200-104295400	Enhancers	Hela-S3	cervix
40	chr9:104295200-104295400	Enhancers	HepG2	liver
41	chr9:104295200-104295400	Enhancers	HMEC	breast
42	chr9:104295200-104295400	Enhancers	HUVEC	blood vessel
43	chr9:104295200-104295400	Enhancers	NH-A	brain
44	chr9:104295200-104295400	Flanking Active TSS	NHDF-Ad	bronchial
45	chr9:104295200-104295400	Enhancers	NHLF	lung
46	chr9:104295200-104295600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr9:104295200-104295600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr9:104295200-104295600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:104295200-104295600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr9:104295200-104295600	Flanking Active TSS	Fetal Heart	heart

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