Variant report

Variant	rs6783175
Chromosome Location	chr3:157831218-157831219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12485440	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12486461	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12696067	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13059066	0.83[EUR][1000 genomes]
rs13061378	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1581408	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1608100	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1608101	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1609525	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1609526	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1610266	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1610267	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1610268	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1730029	0.83[EUR][1000 genomes]
rs1730032	0.83[EUR][1000 genomes]
rs1730044	0.82[EUR][1000 genomes]
rs1915935	0.83[EUR][1000 genomes]
rs2693546	0.83[EUR][1000 genomes]
rs4261830	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4317053	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4346508	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4414801	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4431056	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4602343	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4622858	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4642075	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680411	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680412	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6441174	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6762706	0.83[EUR][1000 genomes]
rs6770442	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6773505	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6789448	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6790608	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6794461	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6797626	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6803532	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6803630	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7614572	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7622971	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7630176	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7647342	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7653039	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs827141	0.81[EUR][1000 genomes]
rs827142	0.81[EUR][1000 genomes]
rs827145	0.81[EUR][1000 genomes]
rs827149	0.83[EUR][1000 genomes]
rs827153	0.83[EUR][1000 genomes]
rs827155	0.83[EUR][1000 genomes]
rs827157	0.83[EUR][1000 genomes]
rs827160	0.83[EUR][1000 genomes]
rs827801	0.81[EUR][1000 genomes]
rs827805	0.83[EUR][1000 genomes]
rs862352	0.83[EUR][1000 genomes]
rs864876	0.83[EUR][1000 genomes]
rs9290020	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9290021	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9814942	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9820954	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9848433	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9862337	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9870745	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9871021	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9881063	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9883891	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6783175	RP11-538P18.2	cis	Artery Tibial	GTEx
rs6783175	RP11-538P18.2	cis	lung	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157828600-157845800	Weak transcription	Spleen	Spleen
2	chr3:157828600-157847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:157828600-157857000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:157828800-157839600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:157828800-157840800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:157828800-157841200	Weak transcription	Left Ventricle	heart
7	chr3:157828800-157847600	Weak transcription	NH-A	brain
8	chr3:157828800-157851000	Weak transcription	Right Ventricle	heart
9	chr3:157829000-157840600	Weak transcription	Fetal Kidney	kidney
10	chr3:157829000-157840800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:157829000-157841000	Weak transcription	Fetal Intestine Large	intestine
12	chr3:157829000-157841200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:157829000-157841400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:157829000-157849400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:157829200-157839600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:157829200-157840000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:157829200-157840600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:157829200-157840800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:157829200-157841200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:157829200-157841200	Weak transcription	Fetal Thymus	thymus
21	chr3:157829200-157841400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:157829200-157841800	Weak transcription	Brain Substantia Nigra	brain
23	chr3:157829200-157842000	Weak transcription	Psoas Muscle	Psoas
24	chr3:157829200-157845400	Weak transcription	HMEC	breast
25	chr3:157829200-157861400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:157829400-157839000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:157829400-157840600	Weak transcription	Fetal Lung	lung
28	chr3:157829600-157839600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:157829600-157840600	Weak transcription	Brain Anterior Caudate	brain
30	chr3:157829600-157840800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:157829600-157841400	Weak transcription	Primary B cells from cord blood	blood
32	chr3:157829800-157840800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:157830000-157835200	Weak transcription	K562	blood
34	chr3:157830000-157835800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:157830000-157839200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:157830000-157840200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:157830000-157840600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:157830000-157840600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:157830000-157840600	Weak transcription	Thymus	Thymus
40	chr3:157830000-157840800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:157830000-157841000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:157830000-157841200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:157830000-157841200	Weak transcription	Hela-S3	cervix
44	chr3:157830000-157841400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:157830000-157841400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:157830000-157843400	Weak transcription	Small Intestine	intestine
47	chr3:157830000-157866400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:157830200-157840600	Weak transcription	Primary T cells from cord blood	blood
49	chr3:157830200-157840800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:157830200-157841400	Weak transcription	HepG2	liver

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