Variant report

Variant	rs1565923
Chromosome Location	chr17:37858678-37858679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75073924..75075938-chr17:37855960..37858891,2	MCF-7	breast:
2	chr17:37857587..37859088-chr17:37859353..37860881,2	K562	blood:
3	chr17:37858020..37860192-chr17:37861876..37864299,2	K562	blood:
4	chr17:37855322..37860162-chr17:37882817..37887032,7	MCF-7	breast:
5	chr17:37854371..37858847-chr17:37859204..37863861,12	MCF-7	breast:
6	chr17:37856670..37858872-chr17:37874487..37877508,3	MCF-7	breast:
7	chr17:37858097..37860300-chr17:37892319..37894495,2	MCF-7	breast:
8	chr17:37842403..37845935-chr17:37858030..37860407,3	K562	blood:
9	chr17:37842383..37849519-chr17:37854521..37862509,17	MCF-7	breast:
10	chr17:37854757..37859429-chr17:37870382..37874180,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000161395	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000141738	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1058808	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11653998	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150298	0.81[CEU][hapmap]
rs12150603	0.81[CEU][hapmap]
rs12940986	0.81[CEU][hapmap]
rs14050	0.90[CEU][hapmap]
rs1476278	0.81[CEU][hapmap]
rs1810132	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2088126	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247862	0.90[CEU][hapmap]
rs2313171	0.81[CEU][hapmap]
rs2517951	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517954	0.95[CEU][hapmap]
rs2517955	0.86[CEU][hapmap]
rs2517956	0.95[CEU][hapmap]
rs2517957	0.82[CEU][hapmap]
rs2517958	0.82[CEU][hapmap]
rs2643194	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2643195	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904766	0.83[ASN][1000 genomes]
rs2934952	0.95[CEU][hapmap]
rs2934953	0.90[CEU][hapmap]
rs2934967	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2934971	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941503	0.95[CEU][hapmap]
rs2941504	0.90[CEU][hapmap]
rs2941505	0.82[CEU][hapmap]
rs2941506	0.81[CEU][hapmap]
rs2941520	0.85[EUR][1000 genomes]
rs2952151	0.90[CEU][hapmap]
rs2952155	0.99[ASN][1000 genomes]
rs2952156	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2952157	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4252627	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795393	0.80[ASN][1000 genomes]
rs8078228	0.81[CEU][hapmap]
rs903501	0.90[CEU][hapmap]
rs903502	0.81[CEU][hapmap]
rs903506	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907087	0.90[CEU][hapmap]
rs907089	0.81[CEU][hapmap]
rs9303274	0.81[CEU][hapmap]
rs9675194	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1565923	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs1565923	PGAP3	cis	Thyroid	GTEx
rs1565923	PGAP3	cis	Heart Left Ventricle	GTEx
rs1565923	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37857000-37872000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:37857600-37861200	Weak transcription	Brain Anterior Caudate	brain
3	chr17:37857600-37863400	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr17:37857800-37861000	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:37857800-37863200	Enhancers	Left Ventricle	heart
6	chr17:37858000-37859400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:37858000-37860800	Weak transcription	Aorta	Aorta
8	chr17:37858000-37861000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:37858000-37861000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:37858000-37861000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:37858000-37861000	Weak transcription	HMEC	breast
12	chr17:37858000-37862200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:37858000-37862400	Genic enhancers	Fetal Stomach	stomach
14	chr17:37858000-37862800	Genic enhancers	Fetal Intestine Large	intestine
15	chr17:37858000-37863200	Weak transcription	HUVEC	blood vessel
16	chr17:37858000-37885200	Weak transcription	Fetal Brain Male	brain
17	chr17:37858000-37885600	Weak transcription	Hela-S3	cervix
18	chr17:37858200-37858800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr17:37858200-37858800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr17:37858200-37859200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
21	chr17:37858200-37859200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:37858200-37859200	Weak transcription	Right Ventricle	heart
23	chr17:37858200-37859800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:37858200-37860000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
25	chr17:37858200-37860200	Flanking Active TSS	HepG2	liver
26	chr17:37858200-37860800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr17:37858200-37860800	Weak transcription	Osteobl	bone
28	chr17:37858200-37861000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:37858200-37861000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:37858200-37861000	Weak transcription	Ovary	ovary
31	chr17:37858200-37861000	Weak transcription	NH-A	brain
32	chr17:37858200-37861200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr17:37858200-37861200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:37858200-37861200	Enhancers	Colonic Mucosa	Colon
35	chr17:37858200-37861200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr17:37858200-37861800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr17:37858200-37862200	Enhancers	Lung	lung
38	chr17:37858200-37862400	Enhancers	Fetal Lung	lung
39	chr17:37858200-37862400	Enhancers	Gastric	stomach
40	chr17:37858200-37862400	Enhancers	Pancreas	Pancrea
41	chr17:37858200-37863200	Weak transcription	Spleen	Spleen
42	chr17:37858200-37863200	Weak transcription	NHLF	lung
43	chr17:37858200-37863600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:37858200-37864000	Enhancers	Liver	Liver
45	chr17:37858200-37864400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:37858200-37882600	Weak transcription	NHDF-Ad	bronchial
47	chr17:37858400-37858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr17:37858400-37858800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:37858400-37858800	Enhancers	A549	lung
50	chr17:37858400-37859000	Enhancers	Fetal Muscle Leg	muscle

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