Variant report

Variant	rs17071716
Chromosome Location	chr13:49011087-49011088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs17069281	1.00[EUR][1000 genomes]
rs17071548	1.00[EUR][1000 genomes]
rs17071560	1.00[EUR][1000 genomes]
rs17071673	1.00[EUR][1000 genomes]
rs17071675	1.00[EUR][1000 genomes]
rs17071714	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3092865	1.00[EUR][1000 genomes]
rs3092883	1.00[EUR][1000 genomes]
rs3901587	1.00[EUR][1000 genomes]
rs41425345	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4151460	1.00[EUR][1000 genomes]
rs4151468	1.00[EUR][1000 genomes]
rs4151487	1.00[EUR][1000 genomes]
rs4151514	1.00[EUR][1000 genomes]
rs4151516	1.00[EUR][1000 genomes]
rs4151527	1.00[EUR][1000 genomes]
rs4151563	1.00[EUR][1000 genomes]
rs4151587	1.00[EUR][1000 genomes]
rs4151621	1.00[EUR][1000 genomes]
rs4151628	1.00[EUR][1000 genomes]
rs4303378	1.00[EUR][1000 genomes]
rs56945534	1.00[EUR][1000 genomes]
rs58318754	1.00[EUR][1000 genomes]
rs59355608	1.00[EUR][1000 genomes]
rs59550884	1.00[EUR][1000 genomes]
rs6561463	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6561467	1.00[EUR][1000 genomes]
rs7316991	1.00[EUR][1000 genomes]
rs7321847	1.00[EUR][1000 genomes]
rs7323517	1.00[EUR][1000 genomes]
rs7324752	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7325924	1.00[EUR][1000 genomes]
rs7329733	1.00[EUR][1000 genomes]
rs7333561	1.00[EUR][1000 genomes]
rs7337056	1.00[EUR][1000 genomes]
rs73487075	1.00[EUR][1000 genomes]
rs73487091	1.00[EUR][1000 genomes]
rs73490880	1.00[EUR][1000 genomes]
rs73493099	1.00[EUR][1000 genomes]
rs74074170	1.00[EUR][1000 genomes]
rs74074184	1.00[EUR][1000 genomes]
rs7981750	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7984036	1.00[EUR][1000 genomes]
rs7984309	1.00[EUR][1000 genomes]
rs7997794	1.00[EUR][1000 genomes]
rs9331954	1.00[EUR][1000 genomes]
rs9332019	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9332048	1.00[EUR][1000 genomes]
rs9332086	1.00[EUR][1000 genomes]
rs9332251	1.00[EUR][1000 genomes]
rs9332256	1.00[EUR][1000 genomes]
rs9332287	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9332296	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9332298	1.00[EUR][1000 genomes]
rs943282	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17071716	PXDN	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48990800-49011600	Weak transcription	Left Ventricle	heart
2	chr13:48990800-49030800	Weak transcription	Ovary	ovary
3	chr13:48991400-49013200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:48991400-49018600	Weak transcription	Thymus	Thymus
5	chr13:48991400-49019200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:48991400-49030600	Weak transcription	Spleen	Spleen
7	chr13:48991800-49018800	Weak transcription	Fetal Thymus	thymus
8	chr13:48994800-49018000	Weak transcription	Primary B cells from cord blood	blood
9	chr13:48997800-49011200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr13:48999000-49024400	Weak transcription	Fetal Muscle Leg	muscle
11	chr13:49001400-49022400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr13:49001400-49024600	Weak transcription	Fetal Intestine Small	intestine
13	chr13:49003000-49012600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:49003600-49011600	Weak transcription	Pancreas	Pancrea
15	chr13:49003600-49023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:49006000-49018000	Weak transcription	Dnd41	blood
17	chr13:49006400-49018800	Weak transcription	GM12878-XiMat	blood
18	chr13:49006600-49011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:49006600-49011600	Weak transcription	Brain Anterior Caudate	brain
20	chr13:49006800-49011200	Weak transcription	HSMM	muscle
21	chr13:49006800-49011600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr13:49006800-49020200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:49006800-49020400	Weak transcription	HSMMtube	muscle
24	chr13:49006800-49020800	Weak transcription	Hela-S3	cervix
25	chr13:49006800-49030400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:49007000-49011200	Weak transcription	Fetal Kidney	kidney
27	chr13:49007000-49027600	Weak transcription	Primary T cells from cord blood	blood
28	chr13:49008000-49028600	Weak transcription	HepG2	liver
29	chr13:49008600-49011400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr13:49008600-49012200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:49008600-49012200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr13:49008800-49030800	Weak transcription	Placenta	Placenta
33	chr13:49009000-49030600	Weak transcription	Gastric	stomach
34	chr13:49009000-49030600	Weak transcription	Lung	lung
35	chr13:49009400-49012800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr13:49009800-49012000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr13:49010200-49011200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr13:49010200-49012000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr13:49010200-49012200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr13:49010200-49012800	Enhancers	Stomach Mucosa	stomach
41	chr13:49010400-49011200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr13:49010400-49012000	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr13:49010400-49012000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr13:49010400-49012200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:49010600-49011200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr13:49010600-49011800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:49010600-49012000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:49010600-49012000	Enhancers	HMEC	breast
49	chr13:49010600-49012200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr13:49010800-49011200	Weak transcription	Primary hematopoietic stem cells	blood

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