Variant report

Variant	rs33953566
Chromosome Location	chr17:37780296-37780297
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	CTCF	chr17:37777426-37780368	A549	lung:	n/a	chr17:37777636-37777645 chr17:37779850-37779868 chr17:37779852-37779865 chr17:37779851-37779867 chr17:37779845-37779866
2	RAD21	chr17:37779496-37780341	HCT-116	colon:	n/a	chr17:37779820-37779834 chr17:37779850-37779862 chr17:37779852-37779866 chr17:37779848-37779867
3	CTCF	chr17:37780180-37780330	NHDF-neo	bronchial:	n/a	n/a
4	ZNF263	chr17:37779510-37780300	HEK293-T-REx	kidney:	n/a	chr17:37780132-37780141
5	SMC3	chr17:37779617-37780336	SK-N-SH	brain:	n/a	chr17:37779852-37779866 chr17:37779852-37779862
6	CTCF	chr17:37780240-37780390	HPF	lung:	n/a	n/a
7	CTCF	chr17:37780180-37780330	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37703730..37705624-chr17:37777887..37780361,14	K562	blood:
2	chr17:37777123..37780362-chr17:37909816..37911514,36	K562	blood:
3	chr17:37777435..37780800-chr17:37803920..37808668,4	K562	blood:
4	chr17:37779913..37781548-chr17:37921179..37923723,2	MCF-7	breast:
5	chr17:37773997..37776613-chr17:37779619..37781489,3	MCF-7	breast:
6	chr17:37703620..37705488-chr17:37779313..37780378,12	MCF-7	breast:
7	chr17:37732171..37732825-chr17:37779402..37780361,2	K562	blood:
8	chr17:37777756..37783081-chr17:37819129..37825010,9	K562	blood:
9	chr17:37776845..37781693-chr17:37790426..37796554,9	K562	blood:
10	chr17:37769208..37773729-chr17:37777189..37781252,6	K562	blood:
11	chr17:37779395..37780335-chr17:37811349..37811933,2	K562	blood:
12	chr17:37778774..37780358-chr17:37893179..37896235,3	K562	blood:
13	chr17:37778202..37782049-chr17:37783082..37786622,6	K562	blood:
14	chr17:37779838..37780411-chr17:37790377..37790904,2	K562	blood:
15	chr17:37775807..37781695-chr17:37822673..37828377,10	K562	blood:

Variant related genes	Relation type
PPP1R1B	TF binding region
ENSG00000214546	Chromatin interaction
ENSG00000131771	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000173991	Chromatin interaction
ENSG00000141744	Chromatin interaction
ENSG00000167258	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1018246	0.87[ASN][1000 genomes]
rs1053651	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10852934	1.00[ASN][1000 genomes]
rs11651497	0.99[ASN][1000 genomes]
rs11658786	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11869286	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12150298	0.87[ASN][1000 genomes]
rs12150603	0.87[ASN][1000 genomes]
rs12453682	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12940986	0.88[ASN][1000 genomes]
rs14050	0.87[ASN][1000 genomes]
rs1476278	0.88[ASN][1000 genomes]
rs1495099	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495100	0.87[ASN][1000 genomes]
rs1495101	0.87[ASN][1000 genomes]
rs1495102	0.87[ASN][1000 genomes]
rs1565920	0.87[ASN][1000 genomes]
rs1565922	0.87[ASN][1000 genomes]
rs1874228	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1877031	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2247862	0.87[ASN][1000 genomes]
rs2271308	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271309	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2313171	0.87[ASN][1000 genomes]
rs2517952	0.80[ASN][1000 genomes]
rs2517953	0.82[ASN][1000 genomes]
rs2517954	0.81[ASN][1000 genomes]
rs2517955	0.80[ASN][1000 genomes]
rs2517956	0.80[ASN][1000 genomes]
rs2517957	0.89[ASN][1000 genomes]
rs2517958	0.89[ASN][1000 genomes]
rs2517959	0.81[ASN][1000 genomes]
rs2934951	0.87[ASN][1000 genomes]
rs2934952	0.87[ASN][1000 genomes]
rs2934953	0.87[ASN][1000 genomes]
rs2934956	0.87[ASN][1000 genomes]
rs2941503	0.87[ASN][1000 genomes]
rs2941504	0.88[ASN][1000 genomes]
rs2941505	0.87[ASN][1000 genomes]
rs2941506	0.87[ASN][1000 genomes]
rs2952151	0.87[ASN][1000 genomes]
rs2952152	0.86[ASN][1000 genomes]
rs3751903	0.99[ASN][1000 genomes]
rs3764352	0.99[ASN][1000 genomes]
rs3764353	0.99[ASN][1000 genomes]
rs3794712	0.95[ASN][1000 genomes]
rs3817160	0.99[ASN][1000 genomes]
rs407307	0.84[ASN][1000 genomes]
rs4794817	0.99[ASN][1000 genomes]
rs4795388	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795389	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795390	0.99[ASN][1000 genomes]
rs732083	0.87[ASN][1000 genomes]
rs732084	0.87[ASN][1000 genomes]
rs8077172	0.87[ASN][1000 genomes]
rs8078228	0.87[ASN][1000 genomes]
rs879606	1.00[ASN][1000 genomes]
rs881844	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs903501	0.88[ASN][1000 genomes]
rs903502	0.87[ASN][1000 genomes]
rs907087	0.87[ASN][1000 genomes]
rs907088	0.87[ASN][1000 genomes]
rs907089	0.87[ASN][1000 genomes]
rs907090	0.87[ASN][1000 genomes]
rs907094	0.99[ASN][1000 genomes]
rs9303274	0.88[ASN][1000 genomes]
rs9675194	0.87[ASN][1000 genomes]
rs9915323	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9972882	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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	92 gene(s)	inside rSNPs	diseases
2	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
3	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
10	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv908208	chr17:37749259-37781849	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv908209	chr17:37749259-37790340	Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv908210	chr17:37761202-37781849	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv908211	chr17:37765047-37782410	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv908212	chr17:37765047-37790340	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs33953566	PGAP3	cis	Thyroid	GTEx
rs33953566	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs33953566	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs33953566	PGAP3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37775000-37782400	Weak transcription	Gastric	stomach
2	chr17:37775200-37781200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:37775200-37782600	Weak transcription	Lung	lung
4	chr17:37775200-37782800	Weak transcription	Right Atrium	heart
5	chr17:37775400-37782800	Weak transcription	Right Ventricle	heart
6	chr17:37777200-37781200	Enhancers	Fetal Brain Male	brain
7	chr17:37777800-37780400	Enhancers	Primary B cells from cord blood	blood
8	chr17:37778000-37780400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:37778400-37780400	Enhancers	Esophagus	oesophagus
10	chr17:37778400-37782600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr17:37778800-37780400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr17:37778800-37780400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr17:37778800-37780400	Enhancers	Fetal Brain Female	brain
14	chr17:37778800-37781400	Enhancers	Duodenum Mucosa	Duodenum
15	chr17:37778800-37781800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr17:37778800-37782400	Enhancers	A549	lung
17	chr17:37778800-37790600	Weak transcription	K562	blood
18	chr17:37779200-37782200	Enhancers	Fetal Lung	lung
19	chr17:37779400-37780400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr17:37779400-37780400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:37779400-37780400	Bivalent Enhancer	HepG2	liver
22	chr17:37779400-37780400	Enhancers	NHEK	skin
23	chr17:37779400-37781000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:37779400-37781000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:37779600-37780400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr17:37779600-37780400	Enhancers	Spleen	Spleen
27	chr17:37779600-37781400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:37779600-37782600	Weak transcription	Fetal Heart	heart
29	chr17:37779800-37780400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr17:37779800-37781600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr17:37780000-37780400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
32	chr17:37780000-37780400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:37780000-37780800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr17:37780000-37781400	Weak transcription	Pancreas	Pancrea
35	chr17:37780200-37780400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr17:37780200-37780400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
37	chr17:37780200-37781000	Weak transcription	Brain Anterior Caudate	brain
38	chr17:37780200-37781400	Weak transcription	Fetal Intestine Large	intestine
39	chr17:37780200-37781800	Weak transcription	Hela-S3	cervix
40	chr17:37780200-37783000	Weak transcription	Ovary	ovary

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