Variant report

Variant	rs1495099
Chromosome Location	chr17:37784464-37784465
allele	C/G
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	RFX5	chr17:37784372-37784528	HepG2	liver:	n/a	chr17:37784440-37784455
2	SIN3A	chr17:37784196-37784694	H1-hESC	embryonic stem cell:	n/a	chr17:37784388-37784397

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37682088..37684502-chr17:37782691..37785037,2	MCF-7	breast:
2	chr17:37784126..37786007-chr17:37898999..37901042,2	K562	blood:

Variant related genes	Relation type
PPP1R1B	TF binding region
ENSG00000167258	Chromatin interaction
ENSG00000141738	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1018246	0.88[ASN][1000 genomes]
rs1053651	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10852934	0.99[ASN][1000 genomes]
rs11651497	0.99[ASN][1000 genomes]
rs11658786	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11869286	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12150298	0.88[ASN][1000 genomes]
rs12150603	0.88[ASN][1000 genomes]
rs12453682	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12940986	0.89[ASN][1000 genomes]
rs14050	0.88[ASN][1000 genomes]
rs1476278	0.89[ASN][1000 genomes]
rs1495100	0.88[ASN][1000 genomes]
rs1495101	0.88[ASN][1000 genomes]
rs1495102	0.88[ASN][1000 genomes]
rs1565920	0.87[ASN][1000 genomes]
rs1565922	0.88[ASN][1000 genomes]
rs1874228	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1877031	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2247862	0.88[ASN][1000 genomes]
rs2271308	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271309	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2313171	0.88[ASN][1000 genomes]
rs2517952	0.81[ASN][1000 genomes]
rs2517953	0.83[ASN][1000 genomes]
rs2517954	0.82[ASN][1000 genomes]
rs2517955	0.81[ASN][1000 genomes]
rs2517956	0.81[ASN][1000 genomes]
rs2517957	0.89[ASN][1000 genomes]
rs2517958	0.89[ASN][1000 genomes]
rs2517959	0.82[ASN][1000 genomes]
rs2517960	0.80[ASN][1000 genomes]
rs2934951	0.88[ASN][1000 genomes]
rs2934952	0.88[ASN][1000 genomes]
rs2934953	0.88[ASN][1000 genomes]
rs2934956	0.88[ASN][1000 genomes]
rs2941503	0.88[ASN][1000 genomes]
rs2941504	0.89[ASN][1000 genomes]
rs2941505	0.88[ASN][1000 genomes]
rs2941506	0.88[ASN][1000 genomes]
rs2952151	0.88[ASN][1000 genomes]
rs2952152	0.87[ASN][1000 genomes]
rs33953566	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751903	1.00[ASN][1000 genomes]
rs3764352	0.99[ASN][1000 genomes]
rs3764353	0.99[ASN][1000 genomes]
rs3794712	0.96[ASN][1000 genomes]
rs3817160	1.00[ASN][1000 genomes]
rs407307	0.85[ASN][1000 genomes]
rs4794817	1.00[ASN][1000 genomes]
rs4795388	0.93[ASN][1000 genomes]
rs4795389	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795390	0.98[ASN][1000 genomes]
rs732083	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs732084	0.88[ASN][1000 genomes]
rs8077172	0.88[ASN][1000 genomes]
rs8078228	0.88[ASN][1000 genomes]
rs879606	0.99[ASN][1000 genomes]
rs881844	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs903501	0.89[ASN][1000 genomes]
rs903502	0.87[ASN][1000 genomes]
rs907087	0.88[ASN][1000 genomes]
rs907088	0.88[ASN][1000 genomes]
rs907089	0.88[ASN][1000 genomes]
rs907090	0.88[ASN][1000 genomes]
rs907094	0.99[ASN][1000 genomes]
rs9303274	0.89[ASN][1000 genomes]
rs9675194	0.88[ASN][1000 genomes]
rs9915323	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9972882	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
12	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
13	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
14	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
15	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
16	esv3438516	chr17:37782451-37785299	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1495099	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs1495099	PGAP3	cis	Thyroid	GTEx
rs1495099	PGAP3	cis	Heart Left Ventricle	GTEx
rs1495099	CRKRS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37778800-37790600	Weak transcription	K562	blood
2	chr17:37782400-37784600	Active TSS	Brain Angular Gyrus	brain
3	chr17:37782600-37784600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
4	chr17:37782600-37784600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
5	chr17:37782800-37785200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
6	chr17:37783200-37784600	Bivalent Enhancer	Fetal Thymus	thymus
7	chr17:37783400-37784600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
8	chr17:37783400-37785000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
9	chr17:37783400-37785200	Active TSS	Pancreas	Pancrea
10	chr17:37783400-37785400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
11	chr17:37783400-37786000	Active TSS	Brain Anterior Caudate	brain
12	chr17:37783400-37786200	Bivalent Enhancer	Fetal Brain Male	brain
13	chr17:37783400-37792200	Weak transcription	Lung	lung
14	chr17:37783600-37784600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
15	chr17:37783600-37785600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
16	chr17:37783600-37790600	Weak transcription	Gastric	stomach
17	chr17:37783800-37784600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
18	chr17:37783800-37785400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr17:37783800-37786000	Weak transcription	Primary B cells from cord blood	blood
20	chr17:37784000-37784600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr17:37784000-37784600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
22	chr17:37784000-37784600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
23	chr17:37784000-37784600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
24	chr17:37784000-37784600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr17:37784000-37784600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr17:37784000-37784600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
27	chr17:37784000-37784600	Flanking Active TSS	Fetal Lung	lung
28	chr17:37784000-37785000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:37784000-37785400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr17:37784000-37786800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:37784000-37789600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:37784200-37784600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:37784200-37784600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
34	chr17:37784200-37784600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr17:37784200-37785000	Enhancers	Fetal Heart	heart
36	chr17:37784200-37785800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:37784200-37786000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
38	chr17:37784200-37786000	Bivalent Enhancer	HepG2	liver
39	chr17:37784400-37784600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr17:37784400-37784600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
41	chr17:37784400-37784600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
42	chr17:37784400-37784600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
43	chr17:37784400-37784600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr17:37784400-37784600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
45	chr17:37784400-37784600	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr17:37784400-37784600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr17:37784400-37784600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr17:37784400-37784600	Enhancers	Right Atrium	heart
49	chr17:37784400-37784600	Flanking Active TSS	Stomach Mucosa	stomach
50	chr17:37784400-37784800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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