Variant report

Variant	rs2517960
Chromosome Location	chr17:37846521-37846522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37842383..37849519-chr17:37854521..37862509,17	MCF-7	breast:
2	chr17:37792073..37793805-chr17:37845398..37847343,2	K562	blood:

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000131748	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1018246	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1053651	0.85[ASN][1000 genomes]
rs11658786	0.84[ASN][1000 genomes]
rs11869286	0.86[ASN][1000 genomes]
rs12150298	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12150603	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12940986	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14050	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1476278	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1495099	0.80[ASN][1000 genomes]
rs1495100	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1495101	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1495102	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1565920	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1565922	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1877031	0.85[ASN][1000 genomes]
rs2247862	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271308	0.84[ASN][1000 genomes]
rs2271309	0.80[ASN][1000 genomes]
rs2313171	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517951	0.86[AMR][1000 genomes]
rs2517952	0.83[ASN][1000 genomes]
rs2517953	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517954	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517956	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517957	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517958	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517959	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904766	0.81[ASN][1000 genomes]
rs2934951	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2934952	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2934953	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2934956	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2941503	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2941504	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2941505	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2941506	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2952151	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2952152	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35734596	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3751903	0.80[ASN][1000 genomes]
rs3817160	0.80[ASN][1000 genomes]
rs407307	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4252627	0.81[AMR][1000 genomes]
rs4794817	0.80[ASN][1000 genomes]
rs732083	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs732084	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8077172	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8078228	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs881844	0.83[ASN][1000 genomes]
rs903501	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs903502	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907087	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs907088	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907089	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907090	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303274	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9675194	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9972882	0.85[ASN][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	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	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
3	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
4	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
5	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
6	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
7	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv908214	chr17:37814224-37861833	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2517960	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs2517960	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2517960	PGAP3	cis	Thyroid	GTEx
rs2517960	PGAP3	cis	Heart Left Ventricle	GTEx
rs2517960	PGAP3	cis	Muscle Skeletal	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37845000-37856000	Weak transcription	Lung	lung
2	chr17:37845200-37854600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:37845200-37854600	Weak transcription	Brain Hippocampus Middle	brain
4	chr17:37845400-37849800	Weak transcription	Brain Angular Gyrus	brain
5	chr17:37845400-37850800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:37845400-37850800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:37845400-37850800	Weak transcription	Fetal Kidney	kidney
8	chr17:37845400-37850800	Weak transcription	Fetal Stomach	stomach
9	chr17:37845400-37851000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr17:37845400-37851000	Weak transcription	Colonic Mucosa	Colon
11	chr17:37845400-37851000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr17:37845400-37851200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:37845400-37851600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:37845400-37854800	Weak transcription	Placenta	Placenta
15	chr17:37845400-37855000	Weak transcription	Brain Substantia Nigra	brain
16	chr17:37845400-37855400	Weak transcription	Left Ventricle	heart
17	chr17:37845400-37855800	Weak transcription	Aorta	Aorta
18	chr17:37845600-37847200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr17:37845600-37847600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr17:37845600-37850200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:37845600-37850800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr17:37845600-37851000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr17:37845600-37851000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr17:37845600-37851000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr17:37845600-37851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:37845600-37851200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr17:37845600-37851200	Weak transcription	Fetal Lung	lung
28	chr17:37845600-37851400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr17:37845600-37851400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr17:37845600-37851400	Weak transcription	Stomach Mucosa	stomach
31	chr17:37845600-37852000	Weak transcription	Pancreas	Pancrea
32	chr17:37845600-37852200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr17:37845600-37852800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr17:37845600-37853400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr17:37845600-37854600	Weak transcription	Primary B cells from cord blood	blood
36	chr17:37845600-37855000	Weak transcription	Fetal Brain Female	brain
37	chr17:37845600-37855400	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:37845600-37855800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:37845600-37855800	Weak transcription	Ovary	ovary
40	chr17:37845600-37855800	Weak transcription	Psoas Muscle	Psoas
41	chr17:37845600-37855800	Weak transcription	Right Ventricle	heart
42	chr17:37845600-37855800	Weak transcription	HSMMtube	muscle
43	chr17:37845600-37856000	Weak transcription	Esophagus	oesophagus
44	chr17:37845600-37856000	Weak transcription	Spleen	Spleen
45	chr17:37845800-37848600	Weak transcription	Fetal Intestine Small	intestine
46	chr17:37845800-37848800	Weak transcription	Fetal Intestine Large	intestine
47	chr17:37845800-37850600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:37845800-37850600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:37845800-37850800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:37845800-37850800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links