Variant report

Variant	rs6540781
Chromosome Location	chr1:213320547-213320548
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10127851	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10465694	0.88[EUR][1000 genomes]
rs10864034	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10864036	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10864038	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1391549	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1391550	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1498357	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1566247	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17020338	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1976333	0.88[EUR][1000 genomes]
rs1995151	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2173398	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2494767	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2647387	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2817976	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2817978	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817981	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2841425	0.89[ASN][1000 genomes]
rs2841427	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2841439	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4655386	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4951476	0.88[EUR][1000 genomes]
rs4951479	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4951662	0.82[EUR][1000 genomes]
rs4951677	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6419469	0.83[AMR][1000 genomes]
rs6419470	0.90[AMR][1000 genomes]
rs6540778	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6540780	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6540782	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657234	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658259	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6666814	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6671872	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679510	0.86[EUR][1000 genomes]
rs6691488	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6692056	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6692144	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6693291	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6699158	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6700169	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7517229	0.80[EUR][1000 genomes]
rs7535369	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7547274	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308430	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9429901	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9429902	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430118	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430120	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430121	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9430122	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9430123	0.91[AMR][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	esv3392967	chr1:213271844-213490132	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv508692	chr1:213309036-213330907	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6540781	ANGEL2	cis	Nerve Tibial	GTEx
rs6540781	ANGEL2	cis	Esophagus Mucosa	GTEx
rs6540781	RPS6KC1	cis	Artery Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213261600-213327400	Weak transcription	Aorta	Aorta
2	chr1:213284600-213349800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:213294200-213321400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:213301000-213371000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:213301000-213374800	Weak transcription	HSMM	muscle
6	chr1:213302600-213358200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:213306200-213331600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:213306600-213323400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:213309600-213329000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:213309600-213336000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:213310000-213345800	Weak transcription	Lung	lung
12	chr1:213310000-213370400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:213310400-213333600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:213310400-213345800	Weak transcription	Ovary	ovary
15	chr1:213312000-213340200	Weak transcription	HSMMtube	muscle
16	chr1:213312200-213340000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:213312200-213343600	Weak transcription	HepG2	liver
18	chr1:213312400-213322200	Weak transcription	Fetal Lung	lung
19	chr1:213312400-213336000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:213312600-213326800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:213312600-213327400	Weak transcription	K562	blood
22	chr1:213313000-213320600	Weak transcription	NHDF-Ad	bronchial
23	chr1:213313000-213320800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:213313400-213322200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:213313800-213336000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:213316000-213340000	Weak transcription	Psoas Muscle	Psoas
27	chr1:213316200-213328400	Weak transcription	Placenta	Placenta
28	chr1:213316400-213336200	Weak transcription	NH-A	brain
29	chr1:213317400-213349600	Weak transcription	Left Ventricle	heart
30	chr1:213317600-213322600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:213317800-213331000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:213317800-213351600	Weak transcription	Fetal Kidney	kidney
33	chr1:213318200-213322000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:213319000-213327200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:213320000-213323600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:213320200-213327400	Weak transcription	Monocytes-CD14+_RO01746	blood

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