Variant report

Variant	rs6469890
Chromosome Location	chr8:121026021-121026022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10110144	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs1051534	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs10955946	1.00[ASN][1000 genomes]
rs10955947	0.96[ASN][1000 genomes]
rs11787175	0.85[CHD][hapmap]
rs11787250	0.85[CHD][hapmap]
rs11986202	0.95[ASN][1000 genomes]
rs11995866	0.82[CHB][hapmap]
rs12546625	0.84[CHD][hapmap]
rs12680396	0.98[ASN][1000 genomes]
rs13272368	0.99[ASN][1000 genomes]
rs1356748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2326429	0.84[ASN][1000 genomes]
rs4053282	0.84[JPT][hapmap]
rs4584180	0.84[ASN][1000 genomes]
rs4870970	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4871719	1.00[ASN][1000 genomes]
rs4871819	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4871821	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4871822	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs4871824	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs4871827	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs58564644	0.98[ASN][1000 genomes]
rs60657932	0.96[ASN][1000 genomes]
rs62528700	0.84[ASN][1000 genomes]
rs6469889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6997067	1.00[ASN][1000 genomes]
rs7833689	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs7836786	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs9642847	0.99[ASN][1000 genomes]
rs9643139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9643140	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6469890	DEPDC6	cis	cerebellum	SCAN
rs6469890	DSCC1	cis	cerebellum	SCAN

Chromatin state (count:46 , 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	chr8:121013200-121029600	Weak transcription	Right Ventricle	heart
6	chr8:121015400-121031600	Weak transcription	Fetal Lung	lung
7	chr8:121015600-121029200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr8:121016000-121031800	Weak transcription	Pancreas	Pancrea
9	chr8:121017000-121067000	Weak transcription	Brain Anterior Caudate	brain
10	chr8:121017200-121029600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr8:121017800-121042000	Weak transcription	Fetal Kidney	kidney
12	chr8:121018200-121031000	Weak transcription	Spleen	Spleen
13	chr8:121019000-121042000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr8:121019800-121027400	Weak transcription	Fetal Stomach	stomach
15	chr8:121020000-121030800	Weak transcription	Gastric	stomach
16	chr8:121020000-121044800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr8:121020000-121046000	Weak transcription	Esophagus	oesophagus
18	chr8:121020200-121027400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr8:121021400-121027600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr8:121021600-121027200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr8:121021600-121029600	Weak transcription	Fetal Muscle Leg	muscle
22	chr8:121021600-121038000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr8:121021600-121042000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr8:121022000-121030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr8:121022000-121031600	Weak transcription	Brain Substantia Nigra	brain
26	chr8:121022200-121026400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr8:121022200-121048200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr8:121022400-121030200	Weak transcription	Brain Hippocampus Middle	brain
29	chr8:121022400-121065400	Weak transcription	Left Ventricle	heart
30	chr8:121022800-121053000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr8:121023000-121027600	Weak transcription	Fetal Intestine Large	intestine
32	chr8:121023800-121027600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr8:121023800-121027600	Weak transcription	Ovary	ovary
34	chr8:121023800-121029800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr8:121024000-121029800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr8:121024200-121029200	Weak transcription	Colon Smooth Muscle	Colon
37	chr8:121024400-121029000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr8:121024400-121029000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:121024600-121029600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr8:121025200-121030200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr8:121025400-121027400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr8:121025600-121026200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr8:121025800-121026200	Strong transcription	Fetal Intestine Small	intestine
44	chr8:121025800-121028000	Strong transcription	Liver	Liver
45	chr8:121025800-121028400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr8:121025800-121033000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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