Variant report

Variant	rs4795393
Chromosome Location	chr17:37893484-37893485
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	CREB1	chr17:37893479-37897560	HepG2	liver:	n/a	n/a
2	NR2F2	chr17:37892854-37893494	HepG2	liver:	n/a	n/a
3	HNF4A	chr17:37893447-37894095	HepG2	liver:	n/a	chr17:37893662-37893677 chr17:37893820-37893832 chr17:37893663-37893676 chr17:37893664-37893676 chr17:37893818-37893833 chr17:37893663-37893671 chr17:37893662-37893670 chr17:37893661-37893669
4	CEBPD	chr17:37893425-37895125	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:37892721-37898234	HepG2	liver:	n/a	n/a
6	ZEB1	chr17:37892050-37897979	HepG2	liver:	n/a	chr17:37897083-37897094 chr17:37894640-37894652 chr17:37895703-37895710 chr17:37897084-37897091 chr17:37897155-37897166 chr17:37897082-37897094 chr17:37892483-37892494 chr17:37897435-37897446
7	HEY1	chr17:37893482-37896135	HepG2	liver:	n/a	chr17:37893723-37893738
8	HEY1	chr17:37893430-37897461	HepG2	liver:	n/a	chr17:37893723-37893738

No.	Distal block	Cell Line	Cell type
1	chr17:37893210..37895843-chr17:38018530..38020744,2	MCF-7	breast:
2	chr17:37886856..37888405-chr17:37890732..37893519,2	K562	blood:
3	chr17:37855582..37857499-chr17:37893190..37897262,3	MCF-7	breast:
4	chr17:37860636..37865251-chr17:37890921..37895460,5	MCF-7	breast:
5	chr17:37892401..37895251-chr20:52209705..52211542,2	MCF-7	breast:
6	chr17:37891597..37894042-chr17:37894356..37897079,2	MCF-7	breast:
7	chr17:37885346..37888543-chr17:37891725..37895938,5	MCF-7	breast:
8	chr17:37858097..37860300-chr17:37892319..37894495,2	MCF-7	breast:
9	chr17:37879887..37888300-chr17:37891591..37897811,12	K562	blood:
10	chr17:37862305..37864519-chr17:37893058..37894844,2	MCF-7	breast:
11	chr17:37790730..37792254-chr17:37891251..37894000,2	K562	blood:
12	chr17:37886957..37890258-chr17:37890918..37893854,3	MCF-7	breast:

Variant related genes	Relation type
GRB7	TF binding region
ENSG00000161405	Chromatin interaction
ENSG00000265178	Chromatin interaction
ENSG00000141736	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000141738	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1058808	0.83[ASN][1000 genomes]
rs11653998	0.83[ASN][1000 genomes]
rs1565923	0.80[ASN][1000 genomes]
rs1810132	0.82[ASN][1000 genomes]
rs2088126	0.84[ASN][1000 genomes]
rs2934967	0.83[ASN][1000 genomes]
rs2934971	0.80[ASN][1000 genomes]
rs2952155	0.81[ASN][1000 genomes]
rs2952156	0.83[ASN][1000 genomes]
rs2952157	0.83[ASN][1000 genomes]
rs4252627	0.83[ASN][1000 genomes]
rs903506	0.84[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	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
2	nsv1056234	chr17:37862605-37909988	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv908219	chr17:37880265-37917633	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4795393	PGAP3	cis	Thyroid	GTEx
rs4795393	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37887200-37893600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:37887200-37893800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr17:37887200-37893800	Weak transcription	HMEC	breast
4	chr17:37887200-37894200	Weak transcription	Small Intestine	intestine
5	chr17:37891600-37893800	Enhancers	Placenta	Placenta
6	chr17:37892000-37893800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:37892000-37893800	Enhancers	Pancreas	Pancrea
8	chr17:37892000-37893800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr17:37892000-37893800	Enhancers	A549	lung
10	chr17:37892000-37894200	Weak transcription	Lung	lung
11	chr17:37892200-37893600	Enhancers	Stomach Mucosa	stomach
12	chr17:37892200-37893800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr17:37892200-37893800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr17:37892200-37893800	Enhancers	Hela-S3	cervix
15	chr17:37892200-37894000	Bivalent Enhancer	Fetal Thymus	thymus
16	chr17:37892400-37893800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:37892400-37893800	Weak transcription	Primary T cells from cord blood	blood
18	chr17:37892400-37893800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:37892600-37893600	Enhancers	Liver	Liver
20	chr17:37892600-37893600	Weak transcription	Esophagus	oesophagus
21	chr17:37892600-37893800	Weak transcription	Spleen	Spleen
22	chr17:37892600-37894200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:37892800-37893600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr17:37892800-37893600	Enhancers	Duodenum Mucosa	Duodenum
25	chr17:37892800-37893600	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr17:37892800-37893800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:37893000-37893600	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr17:37893000-37893800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:37893200-37893600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:37893200-37893800	Weak transcription	Gastric	stomach
31	chr17:37893400-37893600	Flanking Active TSS	Fetal Intestine Large	intestine
32	chr17:37893400-37893800	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr17:37893400-37893800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:37893400-37893800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:37893400-37893800	Active TSS	HepG2	liver
36	chr17:37893400-37893800	Weak transcription	K562	blood

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