Variant report

Variant	rs3912156
Chromosome Location	chr17:20550250-20550251
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	CTCF	chr17:20549859-20550357	SK-N-SH	brain:	n/a	chr17:20550147-20550160
2	PAX5	chr17:20549990-20550272	GM12878	blood:	n/a	chr17:20550258-20550267
3	RAD21	chr17:20549971-20550331	H1-hESC	embryonic stem cell:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
4	CTCF	chr17:20550055-20550282	LNCaP	prostate:	n/a	chr17:20550147-20550160
5	CTCF	chr17:20550040-20550356	Pancreas_OC	pancreas:	n/a	chr17:20550147-20550160
6	CTCF	chr17:20550019-20550357	Lung_OC	lung:	n/a	chr17:20550147-20550160
7	CTCF	chr17:20550041-20550325	ProgFib	skin:	n/a	chr17:20550147-20550160
8	RAD21	chr17:20550068-20550282	ECC-1	luminal epithelium:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
9	CTCF	chr17:20550040-20550347	MCF-7	breast:	n/a	chr17:20550147-20550160
10	CTCF	chr17:20550063-20550303	IMR90	lung:	n/a	chr17:20550147-20550160
11	ZNF143	chr17:20550088-20550319	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr17:20550100-20550250	GM12874	blood:	n/a	chr17:20550147-20550160
13	CTCF	chr17:20550042-20550412	GM10266	blood:	n/a	chr17:20550147-20550160
14	CTCF	chr17:20550011-20550403	K562	blood:	n/a	chr17:20550147-20550160
15	CTCF	chr17:20550031-20550367	A549	lung:	n/a	chr17:20550147-20550160
16	CTCF	chr17:20549966-20550326	GM12878	blood:	n/a	chr17:20550147-20550160
17	CTCF	chr17:20550100-20550250	HCPEpiC	choroid plexus:	n/a	chr17:20550147-20550160
18	FOSL2	chr17:20549974-20550316	HepG2	liver:	n/a	n/a
19	MAZ	chr17:20550135-20550282	K562	blood:	n/a	n/a
20	CTCF	chr17:20550120-20550270	HepG2	liver:	n/a	chr17:20550147-20550160
21	CTCF	chr17:20550058-20550252	GM13977	blood:	n/a	chr17:20550147-20550160
22	CTCF	chr17:20550034-20550323	H1-hESC	embryonic stem cell:	n/a	chr17:20550147-20550160
23	CTCF	chr17:20549817-20550480	A549	lung:	n/a	chr17:20550147-20550160
24	MYC	chr17:20550094-20550260	MCF-7	breast:	n/a	n/a
25	CTCF	chr17:20549930-20550487	A549	lung:	n/a	chr17:20550147-20550160
26	CTCF	chr17:20550042-20550340	MCF-7	breast:	n/a	chr17:20550147-20550160
27	CTCF	chr17:20550020-20550310	HFF-Myc	foreskin:	n/a	chr17:20550147-20550160
28	CTCF	chr17:20550019-20550356	Gliobla	brain:	n/a	chr17:20550147-20550160
29	RAD21	chr17:20550061-20550260	SK-N-SH_RA	brain:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
30	CTCF	chr17:20550100-20550250	GM12878	blood:	n/a	chr17:20550147-20550160
31	RAD21	chr17:20549815-20550375	SK-N-SH	brain:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
32	CTCF	chr17:20550100-20550250	HA-sp	spinal cord:	n/a	chr17:20550147-20550160
33	RAD21	chr17:20549970-20550345	H1-hESC	embryonic stem cell:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
34	CTCF	chr17:20550100-20550250	HBMEC	blood vessel:	n/a	chr17:20550147-20550160
35	CTCF	chr17:20550100-20550250	GM06990	blood:	n/a	chr17:20550147-20550160
36	RAD21	chr17:20550090-20550286	A549	lung:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
37	CTCF	chr17:20550100-20550250	HPAF	blood vessel:	n/a	chr17:20550147-20550160
38	CTCF	chr17:20550120-20550270	Caco-2	colon:	n/a	chr17:20550147-20550160
39	RAD21	chr17:20550052-20550271	K562	blood:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
40	CTCF	chr17:20549965-20550467	A549	lung:	n/a	chr17:20550147-20550160
41	RAD21	chr17:20550062-20550265	GM12878	blood:	n/a	chr17:20550148-20550161 chr17:20550150-20550162
42	CTCF	chr17:20550031-20550332	Fibrobl	skin:	n/a	chr17:20550147-20550160
43	ZNF143	chr17:20550135-20550277	GM12878	blood:	n/a	n/a
44	CTCF	chr17:20550100-20550250	GM12872	blood:	n/a	chr17:20550147-20550160
45	CTCF	chr17:20550034-20550338	MCF-7	breast:	n/a	chr17:20550147-20550160
46	CTCF	chr17:20549951-20550417	K562	blood:	n/a	chr17:20550147-20550160
47	CTCF	chr17:20550042-20550331	Kidney_OC	kidney:	n/a	chr17:20550147-20550160
48	CTCF	chr17:20550100-20550250	GM12875	blood:	n/a	chr17:20550147-20550160
49	CTCF	chr17:20550036-20550338	Hela-S3	cervix:	n/a	chr17:20550147-20550160
50	YY1	chr17:20550056-20550332	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000236504	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12603735	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34070702	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34787317	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3886121	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4082327	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985914	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985917	0.95[ASN][1000 genomes]
rs60500325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065412	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1059504	chr17:20222112-20581021	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv2758445	chr17:20287295-20699840	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	esv2758680	chr17:20287295-20699840	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv907873	chr17:20350968-20550250	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv907874	chr17:20368237-20550250	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv907875	chr17:20368237-20627240	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv1058200	chr17:20369441-20598672	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv907876	chr17:20407149-20550250	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	nsv907878	chr17:20417975-20550250	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv907879	chr17:20417975-20555730	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv907880	chr17:20417975-20591928	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv907881	chr17:20417975-20613642	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
15	nsv1064966	chr17:20431168-20609271	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv907882	chr17:20432757-20608648	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv510703	chr17:20441553-20568237	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv907883	chr17:20487047-20613642	Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv833400	chr17:20497681-20649658	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
22	nsv978390	chr17:20543222-20602211	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3912156	TMEM11	cis	parietal	SCAN
rs3912156	ALDH3A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20549800-20550600	Enhancers	Fetal Heart	heart
2	chr17:20550200-20552000	Weak transcription	Primary B cells from peripheral blood	blood

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