Variant report

Variant	rs13159894
Chromosome Location	chr5:49738788-49738789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10461515	0.80[AFR][1000 genomes]
rs10512892	0.88[ASN][1000 genomes]
rs13167360	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13180931	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13182174	0.97[ASN][1000 genomes]
rs13187179	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13188257	0.80[AFR][1000 genomes]
rs13189219	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16879113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[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];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2137133	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34229766	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34243952	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34293593	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596323	0.80[AFR][1000 genomes]
rs34730675	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34832270	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34902459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906853	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34965128	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34992228	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35066865	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35174411	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35371759	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36047540	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4030575	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62365933	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386168	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62386223	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62387343	0.80[AFR][1000 genomes]
rs62387347	0.80[AFR][1000 genomes]
rs71631462	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3418391	chr5:49734766-49740307	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv3443771	chr5:49734989-49740073	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13159894	PARP8	cis	Adipose Subcutaneous	GTEx
rs13159894	ARL15	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49737400-49739200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr5:49737400-49739200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr5:49737600-49739000	Enhancers	Primary B cells from peripheral blood	blood
4	chr5:49737600-49739200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:49737600-49740800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:49737800-49738800	Enhancers	HMEC	breast
7	chr5:49737800-49739000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr5:49737800-49739000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr5:49737800-49739000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:49737800-49739200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr5:49737800-49739200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr5:49737800-49739200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:49737800-49739200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:49737800-49739200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:49737800-49739200	Enhancers	Fetal Thymus	thymus
16	chr5:49737800-49739400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr5:49737800-49740800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:49737800-49740800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:49737800-49740800	Weak transcription	GM12878-XiMat	blood
20	chr5:49737800-49741200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:49737800-49741400	Weak transcription	Thymus	Thymus
22	chr5:49738000-49739000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr5:49738000-49739200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:49738000-49739200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr5:49738000-49740800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:49738000-49740800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:49738200-49738800	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr5:49738400-49739000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:49738400-49739000	Enhancers	Primary B cells from cord blood	blood
30	chr5:49738400-49739000	Enhancers	Primary T cells from cord blood	blood
31	chr5:49738400-49739600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr5:49738400-49740800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:49738600-49741400	Enhancers	Dnd41	blood

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