Variant report

Variant	rs17413044
Chromosome Location	chr5:53476717-53476718
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10041550	1.00[ASN][1000 genomes]
rs10041555	1.00[ASN][1000 genomes]
rs10043654	1.00[ASN][1000 genomes]
rs10074776	1.00[ASN][1000 genomes]
rs10471883	1.00[ASN][1000 genomes]
rs11739911	1.00[ASN][1000 genomes]
rs11740324	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743996	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155990	1.00[ASN][1000 genomes]
rs13156373	1.00[ASN][1000 genomes]
rs13159846	1.00[ASN][1000 genomes]
rs13162552	0.83[CEU][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171042	1.00[ASN][1000 genomes]
rs13172689	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13183386	1.00[ASN][1000 genomes]
rs13190010	1.00[ASN][1000 genomes]
rs13354296	1.00[ASN][1000 genomes]
rs13354604	1.00[ASN][1000 genomes]
rs13356576	1.00[ASN][1000 genomes]
rs16882546	1.00[ASN][1000 genomes]
rs16882575	1.00[ASN][1000 genomes]
rs16882580	1.00[ASN][1000 genomes]
rs16882609	1.00[ASN][1000 genomes]
rs17266918	1.00[GIH][hapmap]
rs17404688	1.00[GIH][hapmap]
rs28491265	1.00[ASN][1000 genomes]
rs34171374	1.00[ASN][1000 genomes]
rs34430216	1.00[ASN][1000 genomes]
rs34883270	1.00[ASN][1000 genomes]
rs34889997	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35105742	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35486183	1.00[ASN][1000 genomes]
rs35503723	1.00[ASN][1000 genomes]
rs35702491	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35765393	1.00[ASN][1000 genomes]
rs36104210	1.00[ASN][1000 genomes]
rs3846492	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58977090	1.00[ASN][1000 genomes]
rs59853482	1.00[ASN][1000 genomes]
rs60870315	1.00[ASN][1000 genomes]
rs62355131	1.00[ASN][1000 genomes]
rs6450182	1.00[ASN][1000 genomes]
rs66541213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67009061	1.00[ASN][1000 genomes]
rs67012013	1.00[ASN][1000 genomes]
rs67089826	1.00[ASN][1000 genomes]
rs67894567	1.00[ASN][1000 genomes]
rs6859542	1.00[ASN][1000 genomes]
rs6883658	1.00[ASN][1000 genomes]
rs6891928	1.00[ASN][1000 genomes]
rs6892938	1.00[ASN][1000 genomes]
rs71622108	1.00[ASN][1000 genomes]
rs71622110	1.00[ASN][1000 genomes]
rs72752163	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72757857	1.00[ASN][1000 genomes]
rs73120767	1.00[ASN][1000 genomes]
rs7704922	1.00[ASN][1000 genomes]
rs7733332	1.00[ASN][1000 genomes]
rs9292043	1.00[ASN][1000 genomes]
rs9292044	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
19	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
20	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17413044	GPBP1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53433000-53480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr5:53456000-53483000	Weak transcription	Right Ventricle	heart
3	chr5:53466400-53484000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:53466800-53489000	Weak transcription	K562	blood
5	chr5:53467200-53483200	Weak transcription	Primary T cells from cord blood	blood
6	chr5:53469800-53482000	Weak transcription	Psoas Muscle	Psoas
7	chr5:53471800-53476800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:53474000-53481600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:53474200-53490800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:53474400-53480600	Weak transcription	Small Intestine	intestine
11	chr5:53474600-53477600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:53475200-53480600	Weak transcription	Left Ventricle	heart
13	chr5:53475200-53480600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:53475400-53489000	Weak transcription	Right Atrium	heart
15	chr5:53475600-53477200	Weak transcription	Fetal Intestine Large	intestine
16	chr5:53475600-53480200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:53475600-53480600	Weak transcription	Fetal Heart	heart
18	chr5:53476000-53476800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr5:53476000-53477400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:53476000-53477400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:53476000-53477400	Enhancers	Colon Smooth Muscle	Colon
22	chr5:53476000-53477600	Enhancers	Fetal Intestine Small	intestine
23	chr5:53476200-53476800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:53476200-53476800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:53476200-53476800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr5:53476200-53476800	Enhancers	Fetal Muscle Leg	muscle
27	chr5:53476200-53476800	Enhancers	NHDF-Ad	bronchial
28	chr5:53476200-53477000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:53476200-53477200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:53476200-53477400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:53476200-53477600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr5:53476400-53476800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:53476400-53476800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr5:53476400-53477000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:53476400-53477000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:53476400-53477000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr5:53476400-53477000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:53476400-53477000	Enhancers	Fetal Lung	lung
39	chr5:53476400-53477400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr5:53476400-53477400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr5:53476600-53476800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr5:53476600-53476800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr5:53476600-53477000	Enhancers	Cortex derived primary cultured neurospheres	brain

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