Variant report

Variant	rs17694493
Chromosome Location	chr9:22041998-22041999
allele	C/G
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:8)
LncRNA
region (count:0)
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	chr9:22039794-22042948	Hela-S3	cervix:	n/a	n/a
2	SP1	chr9:22041750-22042325	HCT-116	colon:	n/a	n/a
3	JUND	chr9:22041726-22042193	HCT-116	colon:	n/a	n/a
4	NFIC	chr9:22041616-22042431	ECC-1	luminal epithelium:	n/a	n/a
5	GATA3	chr9:22041773-22042302	MCF-7	breast:	n/a	n/a
6	EP300	chr9:22041849-22042208	T-47D	breast:	n/a	n/a
7	STAT3	chr9:22041799-22042064	Hela-S3	cervix:	n/a	chr9:22041996-22042004
8	GTF2F1	chr9:22041748-22042098	Hela-S3	cervix:	n/a	n/a
9	MAX	chr9:22041705-22042178	Hela-S3	cervix:	n/a	n/a
10	MAX	chr9:22041701-22042252	ECC-1	luminal epithelium:	n/a	n/a
11	ESR1	chr9:22041776-22042256	T-47D	breast:	n/a	n/a
12	NR2F2	chr9:22041736-22042251	MCF-7	breast:	n/a	n/a
13	ESR1	chr9:22041797-22042205	T-47D	breast:	n/a	n/a
14	EP300	chr9:22041705-22042308	T-47D	breast:	n/a	n/a
15	SIN3AK20	chr9:22041716-22042222	MCF-7	breast:	n/a	n/a
16	JUND	chr9:22041832-22042364	T-47D	breast:	n/a	n/a
17	SP1	chr9:22041739-22042422	HCT-116	colon:	n/a	n/a
18	CEBPB	chr9:22041767-22042104	MCF-7	breast:	n/a	chr9:22041890-22041903
19	POLR2A	chr9:22041925-22042152	Hela-S3	cervix:	n/a	n/a
20	FOXA1	chr9:22041841-22042246	T-47D	breast:	n/a	n/a
21	GATA3	chr9:22041845-22042213	T-47D	breast:	n/a	n/a
22	RFX5	chr9:22041797-22042194	Hela-S3	cervix:	n/a	n/a
23	RCOR1	chr9:22041803-22042116	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr9:22041798-22042321	MCF-7	breast:	n/a	n/a
25	ESR1	chr9:22041771-22042199	T-47D	breast:	n/a	n/a
26	FOXA1	chr9:22041830-22042216	T-47D	breast:	n/a	n/a
27	TEAD4	chr9:22041793-22042308	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr9:22041786-22042205	ECC-1	luminal epithelium:	n/a	n/a
29	GATA3	chr9:22041766-22042187	T-47D	breast:	n/a	n/a
30	NR3C1	chr9:22041876-22042182	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr9:22041943-22042014	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr9:22041661-22042355	ECC-1	luminal epithelium:	n/a	n/a
33	EP300	chr9:22041752-22042009	Hela-S3	cervix:	n/a	n/a
34	NFIC	chr9:22041711-22042249	ECC-1	luminal epithelium:	n/a	n/a
35	JUND	chr9:22041996-22042204	H1-hESC	embryonic stem cell:	n/a	n/a
36	CEBPB	chr9:22041719-22042074	Hela-S3	cervix:	n/a	chr9:22041890-22041903
37	ESR1	chr9:22041801-22042083	ECC-1	luminal epithelium:	n/a	n/a
38	EP300	chr9:22041842-22042179	MCF-7	breast:	n/a	n/a
39	BRCA1	chr9:22041876-22042163	Hela-S3	cervix:	n/a	n/a
40	TCF12	chr9:22041808-22042334	ECC-1	luminal epithelium:	n/a	n/a
41	EP300	chr9:22041752-22042374	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:22041859..22044589-chr9:22046205..22047807,2	MCF-7	breast:
2	chr9:22040543..22043191-chr9:22050935..22052870,2	MCF-7	breast:
3	chr9:22039593..22042094-chr9:22105940..22108380,2	MCF-7	breast:
4	chr9:22002758..22010749-chr9:22033383..22042446,18	MCF-7	breast:
5	chr9:22034736..22038556-chr9:22039205..22042136,3	MCF-7	breast:
6	chr9:22007719..22013279-chr9:22036472..22044819,13	MCF-7	breast:
7	chr9:22040792..22042968-chr9:22078121..22080153,2	MCF-7	breast:
8	chr9:22040082..22042257-chr9:22102336..22104527,2	MCF-7	breast:

No data

Variant related genes	Relation type
CDKN2B-AS1	TF binding region
ENSG00000240498	Chromatin interaction
ENSG00000147883	Chromatin interaction
ENSG00000215221	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10757262	1.00[CHB][hapmap]
rs11515	1.00[CHB][hapmap]
rs1333034	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17694555	0.91[ASN][1000 genomes]
rs17694572	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17756311	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2069422	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2069426	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2811709	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2811712	1.00[MEX][hapmap]
rs3218018	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3731201	1.00[CHB][hapmap]
rs3731246	1.00[CHB][hapmap]
rs598664	1.00[CHB][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs662463	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs974336	1.00[MEX][hapmap]

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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer	25217961	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17694493	RRAGA	cis	cerebellum	SCAN
rs17694493	CDKN2B	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22036000-22042600	Weak transcription	Esophagus	oesophagus
2	chr9:22036600-22042400	Weak transcription	Pancreas	Pancrea
3	chr9:22036600-22042400	Enhancers	Hela-S3	cervix
4	chr9:22036800-22042800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:22037000-22042200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:22037200-22042400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr9:22037200-22042800	Enhancers	Fetal Intestine Small	intestine
8	chr9:22037400-22042400	Enhancers	NHLF	lung
9	chr9:22037600-22042800	Enhancers	NHEK	skin
10	chr9:22037800-22042600	Enhancers	NHDF-Ad	bronchial
11	chr9:22038200-22044000	Weak transcription	Dnd41	blood
12	chr9:22038600-22042000	Enhancers	Adipose Nuclei	Adipose
13	chr9:22039200-22042200	Enhancers	HSMMtube	muscle
14	chr9:22039200-22042800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:22039200-22042800	Enhancers	HMEC	breast
16	chr9:22039400-22043200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr9:22039600-22042400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:22039800-22042800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:22040000-22042200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:22040000-22042600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:22040000-22042800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:22040000-22042800	Enhancers	HSMM	muscle
23	chr9:22040200-22046000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:22040400-22042200	Enhancers	Osteobl	bone
25	chr9:22040400-22042600	Enhancers	NH-A	brain
26	chr9:22040600-22042400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:22040800-22042000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:22040800-22043200	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr9:22041000-22045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:22041000-22046400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:22041200-22042400	Weak transcription	Fetal Intestine Large	intestine
32	chr9:22041400-22042400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:22041400-22044600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:22041600-22042200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:22041800-22042000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:22041800-22042000	Enhancers	Liver	Liver
37	chr9:22041800-22042000	Enhancers	Placenta	Placenta
38	chr9:22041800-22042000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr9:22041800-22042200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:22041800-22042600	Enhancers	Stomach Mucosa	stomach

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