Variant report

Variant	rs13173294
Chromosome Location	chr5:53463908-53463909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10513040	0.89[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10940361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940364	0.89[CHB][hapmap]
rs11955545	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs11956038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13153747	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13160282	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163481	0.85[ASN][1000 genomes]
rs13164221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13172077	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423607	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1423608	0.88[ASN][1000 genomes]
rs1423609	0.83[ASN][1000 genomes]
rs16882239	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs277332	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs28033	0.88[YRI][hapmap]
rs34060066	0.87[ASN][1000 genomes]
rs34241130	0.94[ASN][1000 genomes]
rs34308112	0.87[ASN][1000 genomes]
rs35264072	0.87[ASN][1000 genomes]
rs36001635	0.87[ASN][1000 genomes]
rs3756486	0.89[CHB][hapmap]
rs3797251	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3797261	0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs3797267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797269	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797270	0.94[ASN][1000 genomes]
rs3843451	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3936611	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57655206	0.98[ASN][1000 genomes]
rs71620000	0.83[ASN][1000 genomes]
rs7718177	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv1015340	chr5:53326385-53471882	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
17	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
18	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
19	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
20	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
21	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13173294	DHX29	cis	cerebellum	SCAN
rs13173294	GPBP1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53409200-53465600	Weak transcription	Fetal Intestine Large	intestine
2	chr5:53425400-53467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:53428000-53471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:53431800-53474000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:53432200-53467600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:53433000-53480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:53442400-53464200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:53442800-53468400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:53443000-53466000	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:53443200-53473800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:53443600-53473800	Weak transcription	Left Ventricle	heart
12	chr5:53443800-53468600	Weak transcription	Adipose Nuclei	Adipose
13	chr5:53444000-53472800	Weak transcription	Lung	lung
14	chr5:53445200-53466000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:53445800-53468000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:53448800-53465600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:53450200-53467600	Weak transcription	Pancreas	Pancrea
18	chr5:53451000-53468600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:53451200-53468000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:53451400-53476200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:53452000-53472800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:53452800-53472400	Weak transcription	Aorta	Aorta
23	chr5:53453000-53465400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr5:53454000-53469400	Weak transcription	Psoas Muscle	Psoas
25	chr5:53456000-53483000	Weak transcription	Right Ventricle	heart
26	chr5:53456200-53468000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:53456600-53467400	Weak transcription	Fetal Intestine Small	intestine
28	chr5:53456600-53473200	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:53456800-53473000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:53458400-53468600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr5:53459000-53465200	Weak transcription	K562	blood
32	chr5:53459800-53469200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:53460000-53468400	Weak transcription	Fetal Stomach	stomach
34	chr5:53460200-53467200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr5:53460400-53467600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:53460600-53473200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:53461800-53475000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:53462000-53464200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:53462400-53467000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:53462800-53465400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:53463000-53468600	Weak transcription	Esophagus	oesophagus
42	chr5:53463400-53465200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:53463400-53465400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:53463400-53467000	Weak transcription	Dnd41	blood
45	chr5:53463400-53467800	Weak transcription	Fetal Heart	heart
46	chr5:53463400-53472400	Weak transcription	Ovary	ovary
47	chr5:53463400-53476200	Weak transcription	NHDF-Ad	bronchial
48	chr5:53463600-53464600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr5:53463600-53465400	Weak transcription	Primary T cells from cord blood	blood
50	chr5:53463600-53465800	Weak transcription	Primary B cells from cord blood	blood

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