Variant report

Variant	rs1072822
Chromosome Location	chr3:43132683-43132684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11129992	0.81[ASN][1000 genomes]
rs12233614	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12485530	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12485578	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12487785	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12497427	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12497602	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523125	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1523126	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566422	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17391761	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17470089	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1815070	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1949583	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1949584	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs488069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55764298	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55819365	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55945909	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55954171	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604033	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6772252	0.85[YRI][hapmap]
rs6785292	0.85[YRI][hapmap]
rs6796161	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796406	0.85[YRI][hapmap]
rs7636537	0.85[YRI][hapmap]
rs7638387	0.85[YRI][hapmap]
rs7640990	1.00[YRI][hapmap]

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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1072822	C3orf39	cis	multi-tissue	Pritchard

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43119600-43135000	Weak transcription	Psoas Muscle	Psoas
2	chr3:43119800-43143800	Weak transcription	Fetal Heart	heart
3	chr3:43122400-43134400	Weak transcription	HepG2	liver
4	chr3:43122400-43145800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:43122600-43145200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:43122800-43133000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:43122800-43134800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:43122800-43136000	Weak transcription	Pancreas	Pancrea
9	chr3:43122800-43136400	Weak transcription	HSMMtube	muscle
10	chr3:43122800-43145600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:43123000-43135200	Weak transcription	Brain Angular Gyrus	brain
12	chr3:43123000-43136000	Weak transcription	Right Ventricle	heart
13	chr3:43123000-43144400	Weak transcription	Fetal Intestine Large	intestine
14	chr3:43123000-43146400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:43123000-43146600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:43123200-43140400	Weak transcription	Gastric	stomach
17	chr3:43123200-43144400	Weak transcription	Spleen	Spleen
18	chr3:43123200-43145000	Weak transcription	Adipose Nuclei	Adipose
19	chr3:43123400-43146400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:43123600-43135000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:43123600-43135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:43123600-43143600	Weak transcription	Lung	lung
23	chr3:43123600-43146600	Weak transcription	Fetal Intestine Small	intestine
24	chr3:43123800-43136400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:43124000-43133400	Weak transcription	Fetal Brain Male	brain
26	chr3:43124000-43134600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:43124200-43135600	Weak transcription	Fetal Brain Female	brain
28	chr3:43124200-43145000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:43124400-43135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:43124400-43136200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:43124400-43136200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:43124400-43144200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:43124400-43146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:43124400-43146600	Weak transcription	Aorta	Aorta
35	chr3:43124600-43138600	Weak transcription	Thymus	Thymus
36	chr3:43124600-43144800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr3:43124600-43146800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:43127000-43144400	Weak transcription	Dnd41	blood
39	chr3:43128400-43134600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:43128600-43134600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:43129000-43139600	Weak transcription	Liver	Liver
42	chr3:43129200-43136000	Weak transcription	Esophagus	oesophagus
43	chr3:43129200-43144000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:43130200-43134600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:43130400-43133800	Weak transcription	Left Ventricle	heart
46	chr3:43130600-43133400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:43130600-43134400	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:43131200-43134600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:43131600-43136600	Weak transcription	Fetal Stomach	stomach
50	chr3:43131600-43145600	Weak transcription	Primary T cells from cord blood	blood

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