Variant report

Variant	rs2517958
Chromosome Location	chr17:37838751-37838752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37820932..37826284-chr17:37838504..37843351,7	K562	blood:
2	chr17:37837216..37838873-chr17:38251603..38253452,2	K562	blood:
3	chr17:37836650..37841918-chr17:37884817..37888421,5	K562	blood:
4	chr17:37837886..37840877-chr17:37841032..37843892,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161395	Chromatin interaction
ENSG00000173991	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000141744	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1018246	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1053651	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10852934	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs11651497	0.89[ASN][1000 genomes]
rs11658786	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11869286	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150298	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12150603	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453682	0.91[YRI][hapmap];0.80[ASN][1000 genomes]
rs12940986	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14050	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1476278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495099	0.89[ASN][1000 genomes]
rs1495100	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495101	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495102	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565920	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565922	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565923	0.82[CEU][hapmap]
rs1810132	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs1874228	0.81[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1877031	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247862	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271308	0.81[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2271309	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2313171	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517951	0.85[AMR][1000 genomes]
rs2517952	0.91[ASN][1000 genomes]
rs2517953	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517954	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517955	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517956	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517959	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517960	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934951	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934952	0.90[CEU][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934953	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934956	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2934971	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2941503	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2941504	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941505	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952151	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2952152	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2952155	0.83[CHB][hapmap]
rs2952156	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs33953566	0.89[ASN][1000 genomes]
rs35734596	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751903	0.89[ASN][1000 genomes]
rs3764352	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3764353	0.89[ASN][1000 genomes]
rs3794712	0.85[ASN][1000 genomes]
rs3817160	0.89[ASN][1000 genomes]
rs407307	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4252627	0.80[AMR][1000 genomes]
rs4794817	0.89[ASN][1000 genomes]
rs4795388	0.83[ASN][1000 genomes]
rs4795389	0.87[ASN][1000 genomes]
rs4795390	0.89[ASN][1000 genomes]
rs732083	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732084	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8077172	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8078228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879606	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs881844	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs903501	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903502	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907087	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907088	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907089	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907090	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907094	0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs9303274	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931992	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs9675194	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9915323	0.82[ASN][1000 genomes]
rs9972882	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv908213	chr17:37807698-37839493	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	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
10	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
rs2517958	PGAP3	cis	Muscle Skeletal	GTEx
rs2517958	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs2517958	PGAP3	cis	Thyroid	GTEx
rs2517958	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2517958	PGAP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37828600-37843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr17:37828800-37839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:37829000-37839600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr17:37829000-37839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr17:37829800-37843600	Weak transcription	NHDF-Ad	bronchial
6	chr17:37830400-37839400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr17:37831800-37843400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:37831800-37843600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:37832000-37839400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:37832200-37844000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:37832400-37839400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:37832600-37839600	Weak transcription	Gastric	stomach
13	chr17:37832600-37843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:37832800-37840400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:37832800-37843600	Weak transcription	NHEK	skin
16	chr17:37833200-37842400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr17:37833600-37839600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:37833600-37843400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:37833600-37843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:37833800-37839400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:37833800-37843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:37834400-37839400	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:37834400-37839600	Weak transcription	Brain Angular Gyrus	brain
24	chr17:37834400-37843000	Strong transcription	Fetal Stomach	stomach
25	chr17:37834400-37843400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:37834400-37843600	Weak transcription	Osteobl	bone
27	chr17:37834600-37843400	Weak transcription	NHLF	lung
28	chr17:37834600-37843600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr17:37834800-37839200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr17:37834800-37839600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr17:37834800-37843600	Weak transcription	Fetal Kidney	kidney
32	chr17:37834800-37843600	Weak transcription	HSMM	muscle
33	chr17:37835000-37839400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:37835000-37840600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr17:37835000-37840800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr17:37835200-37839600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:37835200-37843400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr17:37835600-37842400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr17:37835800-37839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:37836000-37839600	Weak transcription	HSMMtube	muscle
41	chr17:37836000-37842800	Weak transcription	HepG2	liver
42	chr17:37836200-37839400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:37836200-37839400	Weak transcription	K562	blood
44	chr17:37836200-37843600	Weak transcription	Brain Germinal Matrix	brain
45	chr17:37836400-37839400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:37836400-37839600	Weak transcription	Spleen	Spleen
47	chr17:37836400-37840600	Weak transcription	Aorta	Aorta
48	chr17:37836400-37840600	Weak transcription	Esophagus	oesophagus
49	chr17:37836400-37840800	Weak transcription	Pancreas	Pancrea
50	chr17:37836400-37841800	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links