Variant report

Variant	rs29976
Chromosome Location	chr5:52038025-52038026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10512992	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs10805442	0.80[EUR][1000 genomes]
rs11957366	0.80[EUR][1000 genomes]
rs12332623	0.87[ASN][1000 genomes]
rs1626287	0.90[ASN][1000 genomes]
rs1645392	0.80[EUR][1000 genomes]
rs1645393	0.90[ASN][1000 genomes]
rs1645394	0.90[ASN][1000 genomes]
rs164611	0.88[ASN][1000 genomes]
rs164612	0.87[ASN][1000 genomes]
rs164649	0.80[EUR][1000 genomes]
rs164650	0.80[EUR][1000 genomes]
rs164652	0.80[EUR][1000 genomes]
rs164655	0.80[EUR][1000 genomes]
rs1668506	0.90[ASN][1000 genomes]
rs244481	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs244491	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs244493	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs244495	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29977	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs29980	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29982	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351900	0.80[EUR][1000 genomes]
rs351922	0.80[EUR][1000 genomes]
rs351924	0.80[EUR][1000 genomes]
rs351925	0.80[EUR][1000 genomes]
rs351933	0.89[ASN][1000 genomes]
rs351937	0.89[ASN][1000 genomes]
rs351940	0.87[ASN][1000 genomes]
rs352363	0.80[EUR][1000 genomes]
rs352364	0.80[EUR][1000 genomes]
rs352365	0.80[EUR][1000 genomes]
rs39811	0.85[ASN][1000 genomes]
rs599698	0.88[ASN][1000 genomes]
rs651393	0.88[ASN][1000 genomes]
rs657796	0.88[ASN][1000 genomes]
rs658771	0.88[ASN][1000 genomes]
rs664248	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1027410	chr5:52022713-52103360	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs29976	LY86AS	trans	cerebellum	SCAN
rs29976	PPAP2A	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52029600-52039200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:52033200-52039400	Enhancers	Primary T cells from cord blood	blood
3	chr5:52034400-52038400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:52034400-52039200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:52034400-52040200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:52034600-52038200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:52035000-52038200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:52035200-52038200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:52036600-52039200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:52036600-52040000	Weak transcription	Fetal Stomach	stomach
11	chr5:52036800-52039000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:52037000-52041600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:52037000-52042000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr5:52037200-52041600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr5:52037200-52041600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:52037200-52042000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr5:52037400-52039600	Enhancers	Small Intestine	intestine
18	chr5:52037400-52041000	Enhancers	Dnd41	blood
19	chr5:52037400-52042200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:52037600-52041000	Enhancers	HUVEC	blood vessel
21	chr5:52037600-52041200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:52037600-52042600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr5:52037800-52040200	Enhancers	Fetal Lung	lung
24	chr5:52037800-52042200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:52038000-52039000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr5:52038000-52039000	Weak transcription	Fetal Thymus	thymus
27	chr5:52038000-52039200	Weak transcription	Aorta	Aorta
28	chr5:52038000-52041000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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