Variant report

Variant	rs12477879
Chromosome Location	chr2:112969865-112969866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10183121	0.92[YRI][hapmap]
rs10864901	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11123133	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11676628	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11679986	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11682795	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11685462	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11685514	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11687980	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11688511	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11689858	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11691239	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11693294	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11695974	0.93[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12474447	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4516428	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55798617	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55802705	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55821286	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55861985	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56044884	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56048537	0.81[AMR][1000 genomes]
rs6711180	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6722612	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6747639	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6751146	0.93[YRI][hapmap]
rs6757750	0.84[YRI][hapmap]
rs6759283	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6760316	0.91[AFR][1000 genomes]
rs6761440	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831633	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831634	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831636	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831638	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72831639	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72831641	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72831642	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72831649	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831651	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831658	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831660	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831662	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72831664	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72831685	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72831688	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72833410	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833412	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833413	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833414	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833415	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72833428	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72833431	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72833432	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7586893	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7587316	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7596661	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7599551	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv874866	chr2:112906599-112991098	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	5 gene(s)	inside rSNPs	diseases
6	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12477879	RGPD8	cis	Nerve Tibial	GTEx
rs12477879	RGPD8	cis	Esophagus Mucosa	GTEx
rs12477879	RGPD8	cis	Esophagus Muscularis	GTEx
rs12477879	RGPD8	cis	Artery Aorta	GTEx
rs12477879	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs12477879	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs12477879	RGPD8	cis	Artery Tibial	GTEx
rs12477879	RGPD8	cis	Thyroid	GTEx
rs12477879	RGPD8	cis	lung	GTEx
rs12477879	RGPD8	cis	Adipose Subcutaneous	GTEx
rs12477879	RGPD8	cis	Muscle Skeletal	GTEx
rs12477879	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs12477879	RGPD8	cis	Whole Blood	GTEx
rs12477879	RGPD8	cis	Heart Left Ventricle	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112914600-112972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:112945200-112970600	Weak transcription	Fetal Stomach	stomach
3	chr2:112959600-112987000	Weak transcription	Osteobl	bone
4	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:112962400-112979000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:112963200-112978800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:112964000-112973600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:112964800-112970400	Weak transcription	Dnd41	blood
9	chr2:112965200-112972200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:112965600-112971600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:112965600-112972200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:112965800-112971800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:112965800-112972000	Weak transcription	Lung	lung
14	chr2:112965800-112972200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:112966600-112970400	Strong transcription	Primary T cells from cord blood	blood
16	chr2:112966600-112972200	Weak transcription	Brain Anterior Caudate	brain
17	chr2:112967600-112970200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:112967600-112972000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:112967600-112972600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:112967600-112977000	Weak transcription	Fetal Kidney	kidney
21	chr2:112967800-112971800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr2:112967800-112972000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:112967800-112977600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:112967800-112978000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:112967800-112986600	Weak transcription	NHEK	skin
26	chr2:112967800-112987000	Weak transcription	Aorta	Aorta
27	chr2:112968000-112971200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:112968000-112972800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:112968000-112973600	Weak transcription	A549	lung
30	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
31	chr2:112968200-112970200	Strong transcription	Brain Hippocampus Middle	brain
32	chr2:112968200-112970600	Weak transcription	Fetal Intestine Large	intestine
33	chr2:112968200-112972200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:112968200-112972200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:112968200-112972200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:112968200-112972800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:112968200-112978800	Weak transcription	Fetal Lung	lung
38	chr2:112968200-112979600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:112968200-112999000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:112968200-113004000	Weak transcription	Fetal Brain Male	brain
41	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
42	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
43	chr2:112968400-112970400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:112968400-112971800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:112968400-112972000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:112968400-112972000	Weak transcription	GM12878-XiMat	blood
47	chr2:112968400-112972200	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:112968400-112972200	Weak transcription	HMEC	breast
49	chr2:112968400-112978800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:112968400-112981400	Weak transcription	K562	blood

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