Variant report

Variant	rs16879113
Chromosome Location	chr5:49710710-49710711
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10461515	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10512892	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13159894	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]
rs13167360	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13180931	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13182174	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13187179	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13188257	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13189219	0.86[EUR][1000 genomes]
rs2137133	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34229766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34243952	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34293593	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34596323	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34730675	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34832270	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34902459	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34906853	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34965128	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34992228	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35066865	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35174411	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35371759	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35700380	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36047540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36184257	0.84[EUR][1000 genomes]
rs4030575	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62365933	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62386168	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62386223	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62387343	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62387346	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62387347	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71631462	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16879113	ARL15	cis	parietal	SCAN
rs16879113	PARP8	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49682000-49719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:49697400-49723400	Weak transcription	HSMM	muscle
5	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:49698200-49711600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:49701000-49711400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:49703200-49719000	Weak transcription	HMEC	breast
10	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:49703400-49711800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr5:49703600-49711400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr5:49704400-49711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:49705400-49715800	Weak transcription	Fetal Intestine Large	intestine
16	chr5:49707200-49715000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr5:49708600-49711000	Weak transcription	Dnd41	blood
18	chr5:49709400-49713000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr5:49709400-49715000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:49709600-49715000	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr5:49709600-49716800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:49709800-49711800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:49709800-49712000	Enhancers	Primary B cells from cord blood	blood
24	chr5:49709800-49712000	Enhancers	Primary T cells from cord blood	blood
25	chr5:49709800-49712600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr5:49709800-49715000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr5:49709800-49715600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr5:49710000-49713200	Enhancers	Primary B cells from peripheral blood	blood
29	chr5:49710000-49714600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr5:49710000-49715000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:49710000-49715200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr5:49710400-49712400	Weak transcription	Fetal Thymus	thymus
33	chr5:49710400-49712600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:49710600-49713200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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