Variant report

Variant	rs34572942
Chromosome Location	chr17:16346484-16346485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:164)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:164 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr17:16346482-16346657	K562	blood:	n/a	n/a
2	POLR2A	chr17:16344170-16348258	GM12892	blood:	n/a	n/a
3	POLR2A	chr17:16344955-16348227	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:16341287-16348457	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:16341231-16355258	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:16341181-16348546	GM12892	blood:	n/a	n/a
7	POLR2A	chr17:16345056-16348120	GM12891	blood:	n/a	n/a
8	POLR2A	chr17:16345683-16347975	ProgFib	skin:	n/a	n/a
9	MTA3	chr17:16345323-16348310	GM12878	blood:	n/a	n/a
10	ZBTB33	chr17:16345442-16347664	A549	lung:	n/a	n/a
11	POLR2A	chr17:16341449-16348238	GM12878	blood:	n/a	n/a
12	POLR2A	chr17:16344102-16348326	HUVEC	blood vessel:	n/a	n/a
13	FOXM1	chr17:16345893-16347850	GM12878	blood:	n/a	n/a
14	ATF3	chr17:16345166-16346494	A549	lung:	n/a	n/a
15	POLR2A	chr17:16341417-16352882	K562	blood:	n/a	n/a
16	POLR2A	chr17:16344327-16348137	GM19099	blood:	n/a	n/a
17	POLR2A	chr17:16341426-16350683	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr17:16341457-16348329	Hela-S3	cervix:	n/a	n/a
19	JUND	chr17:16346435-16348008	SK-N-SH	brain:	n/a	n/a
20	MAX	chr17:16345400-16348228	A549	lung:	n/a	n/a
21	ATF2	chr17:16345509-16346761	H1-hESC	embryonic stem cell:	n/a	n/a
22	PBX3	chr17:16346079-16348229	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr17:16341402-16348159	K562	blood:	n/a	n/a
24	NFATC1	chr17:16345371-16348250	GM12878	blood:	n/a	n/a
25	POLR2A	chr17:16345354-16346834	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr17:16345426-16348166	HEK293	kidney:	n/a	n/a
27	STAT5A	chr17:16345401-16348157	GM12878	blood:	n/a	n/a
28	BRCA1	chr17:16345141-16346785	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr17:16345447-16346997	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr17:16341463-16352887	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr17:16345350-16348219	A549	lung:	n/a	n/a
32	ATF2	chr17:16346347-16346770	GM12878	blood:	n/a	n/a
33	POLR2A	chr17:16341555-16352948	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr17:16344198-16348289	K562	blood:	n/a	n/a
35	ATF2	chr17:16345210-16347277	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF263	chr17:16345013-16347877	HEK293-T-REx	kidney:	n/a	chr17:16346992-16347013
37	POLR2A	chr17:16344168-16348295	HepG2	liver:	n/a	n/a
38	POLR2A	chr17:16344218-16348200	HepG2	liver:	n/a	n/a
39	POLR2A	chr17:16344285-16348336	PBDE	blood:	n/a	n/a
40	TBL1XR1	chr17:16346398-16346771	K562	blood:	n/a	n/a
41	GATA3	chr17:16345827-16348030	A549	lung:	n/a	n/a
42	POLR2A	chr17:16344255-16348258	HepG2	liver:	n/a	n/a
43	GTF2F1	chr17:16345973-16346843	Hela-S3	cervix:	n/a	n/a
44	HEY1	chr17:16344219-16348073	K562	blood:	n/a	n/a
45	MYBL2	chr17:16345394-16347082	HepG2	liver:	n/a	n/a
46	RUNX3	chr17:16346426-16346802	GM12878	blood:	n/a	n/a
47	POLR2A	chr17:16345431-16348300	HepG2	liver:	n/a	n/a
48	FOXM1	chr17:16346345-16347005	GM12878	blood:	n/a	n/a
49	SIN3AK20	chr17:16345583-16347761	A549	lung:	n/a	n/a
50	TEAD4	chr17:16345370-16347841	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16345715..16347819-chr17:16375734..16378400,2	MCF-7	breast:
2	chr17:16306085..16308044-chr17:16345909..16348018,2	K562	blood:
3	chr17:16187896..16189680-chr17:16346072..16348174,2	MCF-7	breast:
4	chr17:16346147..16346731-chr7:73064929..73065655,2	Hela-S3	cervix:
5	chr17:16282507..16286910-chr17:16340967..16348886,17	K562	blood:
6	chr17:16267186..16269021-chr17:16346111..16348065,2	MCF-7	breast:
7	chr17:16265967..16268292-chr17:16345607..16348010,2	K562	blood:
8	chr17:16346081..16346929-chr5:78280517..78281145,2	Hela-S3	cervix:
9	chr17:16344635..16348382-chr17:16375517..16378803,3	K562	blood:
10	chr17:16346183..16347086-chr17:72977814..72978912,3	Hela-S3	cervix:
11	chr17:16345883..16346559-chr5:131892666..131893186,2	Hela-S3	cervix:
12	chr17:16346423..16347301-chr22:38965716..38966432,2	NB4	blood:
13	chr17:16344731..16348160-chr17:16400041..16403043,3	MCF-7	breast:
14	chr17:16282813..16296019-chr17:16339657..16347255,30	K562	blood:
15	chr17:16346470..16347308-chr7:5569542..5570056,2	Hela-S3	cervix:
16	chr17:16282599..16286966-chr17:16344575..16348977,7	MCF-7	breast:
17	chr12:52627559..52628228-chr17:16346399..16347385,2	Hela-S3	cervix:
18	chr17:16280089..16281787-chr17:16345000..16347906,2	K562	blood:
19	chr17:16345956..16349189-chr17:16418273..16421633,4	K562	blood:
20	chr17:16316817..16323346-chr17:16340136..16347615,14	MCF-7	breast:
21	chr17:16345752..16348738-chr17:16386429..16389411,2	MCF-7	breast:
22	chr17:16282005..16293050-chr17:16338399..16351573,30	MCF-7	breast:
23	chr17:16345713..16346553-chr7:5564890..5565677,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000266651	TF binding region
ENSG00000265401	Chromatin interaction
ENSG00000264739	Chromatin interaction
ENSG00000113522	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000100206	Chromatin interaction
ENSG00000170315	Chromatin interaction
ENSG00000187688	Chromatin interaction
ENSG00000265095	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11078342	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11078343	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11078344	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11078345	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11653149	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654069	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11867498	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11869614	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11870279	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11871017	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11871929	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11871958	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11871963	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12936240	0.84[AMR][1000 genomes]
rs12938294	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12940078	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17552310	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17715447	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34166276	0.84[AMR][1000 genomes]
rs34192401	0.84[AMR][1000 genomes]
rs34419652	0.84[AMR][1000 genomes]
rs34577506	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34779276	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34793697	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34982046	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35034622	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35247166	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35269706	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35377488	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35474528	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35540454	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35774281	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36117589	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56097826	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7217211	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs941411	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv1065254	chr17:16252880-16389930	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
9	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	occipital cortex	BrainEAC
rs34572942	C17orf45	Cis_1M	lymphoblastoid	RTeQTL
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	frontal cortex	BrainEAC
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	temporal cortex	BrainEAC
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	brain	BrainEAC
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	cerebellar cortex	BrainEAC
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	intralobular white matter	BrainEAC
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	hippocampus	BrainEAC
rs34572942	NCRNA00188,SNORD49A,SNORD65	cis	inferior olivary nucleus	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16342400-16347000	Transcr. at gene 5' and 3'	A549	lung
2	chr17:16342800-16346600	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr17:16342800-16346800	Transcr. at gene 5' and 3'	K562	blood
4	chr17:16343000-16348000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr17:16343800-16347000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:16343800-16347600	Genic enhancers	Left Ventricle	heart
7	chr17:16343800-16347800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:16343800-16347800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:16343800-16348000	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr17:16343800-16348000	Genic enhancers	Brain Cingulate Gyrus	brain
11	chr17:16343800-16349800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
12	chr17:16343800-16350200	Genic enhancers	Fetal Muscle Leg	muscle
13	chr17:16343800-16354600	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:16343800-16363400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr17:16344000-16347800	Genic enhancers	Stomach Mucosa	stomach
16	chr17:16344000-16348000	Genic enhancers	Liver	Liver
17	chr17:16344000-16348000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr17:16344000-16348000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr17:16344000-16348200	Genic enhancers	Adipose Nuclei	Adipose
20	chr17:16344000-16348200	Genic enhancers	Lung	lung
21	chr17:16344000-16349800	Genic enhancers	Esophagus	oesophagus
22	chr17:16344200-16346800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr17:16344200-16348000	Genic enhancers	Pancreas	Pancrea
24	chr17:16344200-16348000	Strong transcription	Rectal Smooth Muscle	rectum
25	chr17:16344400-16346800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr17:16344400-16346800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:16344400-16346800	Strong transcription	Brain Substantia Nigra	brain
28	chr17:16344400-16347000	Strong transcription	Ovary	ovary
29	chr17:16344400-16347400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
30	chr17:16344400-16347600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:16344400-16347800	Genic enhancers	Gastric	stomach
32	chr17:16344400-16348000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr17:16344400-16348000	Genic enhancers	Spleen	Spleen
34	chr17:16344400-16348200	Genic enhancers	Fetal Brain Female	brain
35	chr17:16344600-16346600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr17:16344600-16346600	Strong transcription	Brain Germinal Matrix	brain
37	chr17:16344600-16347000	Strong transcription	HSMMtube	muscle
38	chr17:16344600-16348200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr17:16344600-16353000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr17:16344600-16372800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr17:16344800-16347000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr17:16344800-16352800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr17:16344800-16355000	Strong transcription	Fetal Stomach	stomach
44	chr17:16345000-16347200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:16345000-16347600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr17:16345000-16348000	Genic enhancers	HMEC	breast
47	chr17:16345000-16349800	Enhancers	Fetal Heart	heart
48	chr17:16345000-16350400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr17:16345000-16352600	Strong transcription	Aorta	Aorta
50	chr17:16345000-16354600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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