Variant report

Variant	rs867709
Chromosome Location	chr8:121035954-121035955
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11986039	0.98[ASN][1000 genomes]
rs11986628	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11993265	0.96[ASN][1000 genomes]
rs1401810	0.98[ASN][1000 genomes]
rs1401812	0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1401813	0.80[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1543200	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543201	0.99[ASN][1000 genomes]
rs1850886	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1879150	0.99[ASN][1000 genomes]
rs2037342	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037343	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037344	0.95[CEU][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2139438	0.98[ASN][1000 genomes]
rs2139439	0.99[ASN][1000 genomes]
rs2176748	0.99[ASN][1000 genomes]
rs2176749	0.99[ASN][1000 genomes]
rs2176751	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2271900	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2326428	0.99[ASN][1000 genomes]
rs2326430	0.99[ASN][1000 genomes]
rs2326433	0.96[ASN][1000 genomes]
rs2326434	0.86[ASN][1000 genomes]
rs2875927	0.99[ASN][1000 genomes]
rs2875932	0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28885745	0.99[ASN][1000 genomes]
rs4053282	0.85[CEU][hapmap]
rs4086915	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4348544	0.96[ASN][1000 genomes]
rs4520205	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4621850	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4871031	0.99[ASN][1000 genomes]
rs4871032	0.98[ASN][1000 genomes]
rs4871824	0.85[CEU][hapmap]
rs6469882	0.99[ASN][1000 genomes]
rs6469888	0.99[ASN][1000 genomes]
rs6469891	0.98[ASN][1000 genomes]
rs6469893	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6985424	0.86[ASN][1000 genomes]
rs6997910	0.81[ASN][1000 genomes]
rs7012522	0.98[ASN][1000 genomes]
rs7386139	0.99[ASN][1000 genomes]
rs7387672	0.99[ASN][1000 genomes]
rs7464941	0.97[ASN][1000 genomes]
rs7813264	1.00[ASN][1000 genomes]
rs7817075	1.00[ASN][1000 genomes]
rs7817379	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7821583	1.00[ASN][1000 genomes]
rs7821842	1.00[ASN][1000 genomes]
rs7822000	1.00[ASN][1000 genomes]
rs7822384	0.85[ASN][1000 genomes]
rs7824637	0.92[ASN][1000 genomes]
rs7829279	0.99[ASN][1000 genomes]
rs7832657	1.00[ASN][1000 genomes]
rs7840668	0.91[ASN][1000 genomes]
rs7845541	0.96[ASN][1000 genomes]
rs7846263	0.98[ASN][1000 genomes]
rs9297609	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv891419	chr8:120990455-121047798	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs867709	VAMP1	cis	Cerebellum	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120995600-121038400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr8:121004000-121048000	Weak transcription	Stomach Mucosa	stomach
3	chr8:121004600-121041400	Weak transcription	Brain Angular Gyrus	brain
4	chr8:121005200-121045800	Weak transcription	Psoas Muscle	Psoas
5	chr8:121017000-121067000	Weak transcription	Brain Anterior Caudate	brain
6	chr8:121017800-121042000	Weak transcription	Fetal Kidney	kidney
7	chr8:121019000-121042000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:121020000-121044800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr8:121020000-121046000	Weak transcription	Esophagus	oesophagus
10	chr8:121021600-121038000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:121021600-121042000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr8:121022200-121048200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:121022400-121065400	Weak transcription	Left Ventricle	heart
14	chr8:121022800-121053000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:121026400-121036000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr8:121028000-121043800	Weak transcription	Liver	Liver
17	chr8:121029800-121048400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr8:121030600-121037000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr8:121031200-121036200	Weak transcription	Spleen	Spleen
20	chr8:121032000-121039600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:121032000-121041800	Weak transcription	Brain Substantia Nigra	brain
22	chr8:121032000-121058000	Weak transcription	Pancreas	Pancrea
23	chr8:121032200-121036800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:121032200-121036800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr8:121032200-121041800	Weak transcription	Brain Hippocampus Middle	brain
26	chr8:121032200-121041800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr8:121032200-121044800	Weak transcription	Gastric	stomach
28	chr8:121032400-121036600	Weak transcription	Fetal Intestine Large	intestine
29	chr8:121032400-121044800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:121033000-121036000	Weak transcription	Fetal Muscle Leg	muscle
31	chr8:121033000-121046200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr8:121033800-121039400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr8:121034400-121036800	Weak transcription	Fetal Stomach	stomach
34	chr8:121034600-121039000	Enhancers	Colon Smooth Muscle	Colon
35	chr8:121034800-121038200	Enhancers	Ovary	ovary
36	chr8:121035400-121037800	Weak transcription	Fetal Intestine Small	intestine
37	chr8:121035600-121036400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr8:121035800-121036800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr8:121035800-121037800	Weak transcription	Rectal Smooth Muscle	rectum

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