Variant report

Variant	rs10076833
Chromosome Location	chr5:114576598-114576599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10045548	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10059069	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10079380	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11745083	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11745170	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs17640052	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303001	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs267298	0.81[TSI][hapmap]
rs3805580	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3805581	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805586	0.90[GIH][hapmap]
rs62383168	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6594882	0.96[ASN][1000 genomes]
rs6594883	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs67276221	0.99[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6878733	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6886102	0.82[CEU][hapmap];0.84[LWK][hapmap];0.86[EUR][1000 genomes]
rs7706217	0.81[CEU][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes]
rs7725831	1.00[ASW][hapmap];0.82[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9326954	0.82[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1029371	chr5:114541428-114590891	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10076833	TRIM36	cis	multi-tissue	Pritchard
rs10076833	CCDC112	cis	parietal	SCAN
rs10076833	PGGT1B	cis	normal skin	skin_eQTL
rs10076833	PGGT1B	cis	lymphoblastoid	seeQTL
rs10076833	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs10076833	PGGT1B	cis	multi-tissue	Pritchard
rs10076833	ENSG00000164219	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
2	chr5:114539200-114580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:114543800-114577800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:114546800-114578000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:114547600-114577600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:114547800-114578400	Weak transcription	Esophagus	oesophagus
7	chr5:114547800-114596600	Weak transcription	Brain Germinal Matrix	brain
8	chr5:114548400-114596800	Weak transcription	K562	blood
9	chr5:114549400-114597200	Weak transcription	Aorta	Aorta
10	chr5:114552200-114581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:114555800-114579800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr5:114556200-114578000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:114557000-114577400	Weak transcription	Fetal Heart	heart
14	chr5:114557800-114579400	Weak transcription	Gastric	stomach
15	chr5:114558000-114579400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:114559000-114587600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:114559400-114578200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:114559400-114579400	Weak transcription	Spleen	Spleen
19	chr5:114560600-114577400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr5:114562400-114577600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:114562400-114577600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:114563200-114578400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:114563400-114578600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:114563400-114591600	Weak transcription	Brain Anterior Caudate	brain
25	chr5:114563400-114597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:114565200-114597400	Weak transcription	Colonic Mucosa	Colon
27	chr5:114567400-114590600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:114567800-114589800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:114568800-114577600	Weak transcription	NHEK	skin
30	chr5:114569600-114577600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:114569600-114578000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:114569600-114578200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:114569800-114577200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr5:114570000-114577000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr5:114570000-114577400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr5:114570000-114577600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:114570000-114577800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:114570200-114577800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:114570200-114579800	Strong transcription	Primary B cells from cord blood	blood
40	chr5:114570400-114577000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:114570400-114577800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:114570600-114576800	Strong transcription	Liver	Liver
43	chr5:114570600-114577000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:114570600-114577000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:114570600-114577400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:114570600-114577600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:114570800-114577000	Strong transcription	Placenta	Placenta
48	chr5:114571000-114577000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:114571000-114577800	Strong transcription	Fetal Thymus	thymus
50	chr5:114571600-114577400	Strong transcription	Adipose Nuclei	Adipose

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