Variant report

Variant	rs6669008
Chromosome Location	chr1:114166561-114166562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10858011	0.82[CHD][hapmap]
rs1113523	0.82[CHD][hapmap]
rs1146182	0.82[CHD][hapmap]
rs1146187	0.85[CHD][hapmap]
rs1217192	0.82[CHD][hapmap]
rs1217200	0.85[CHD][hapmap]
rs1217201	0.82[CHD][hapmap]
rs1217226	0.82[CHD][hapmap]
rs1217227	0.82[CHD][hapmap]
rs1217228	0.82[CHD][hapmap]
rs1217234	0.82[CHD][hapmap]
rs1217236	0.80[CHD][hapmap]
rs1230658	0.85[CHD][hapmap]
rs1230659	0.84[CHD][hapmap]
rs12565589	0.85[CHD][hapmap]
rs12723023	0.83[AFR][1000 genomes]
rs12739970	0.83[AFR][1000 genomes]
rs12753075	0.81[AFR][1000 genomes]
rs1743605	0.85[CHD][hapmap]
rs1777237	0.85[CHD][hapmap]
rs1777241	0.84[CHD][hapmap]
rs1891969	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839331	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs55912359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704054	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514649	1.00[YRI][hapmap]
rs7517631	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	nsv1012324	chr1:114135133-114206843	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6669008	CD58	cis	cerebellum	SCAN
rs6669008	ADORA3	cis	parietal	SCAN
rs6669008	PHTF1	cis	cerebellum	SCAN
rs6669008	MAGI3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114100600-114173400	Weak transcription	Gastric	stomach
2	chr1:114119200-114172400	Weak transcription	Pancreas	Pancrea
3	chr1:114119200-114173000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:114124400-114172400	Weak transcription	Aorta	Aorta
5	chr1:114140600-114172800	Weak transcription	Colonic Mucosa	Colon
6	chr1:114151400-114172600	Weak transcription	Ovary	ovary
7	chr1:114153600-114168400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:114154000-114172400	Weak transcription	Fetal Stomach	stomach
9	chr1:114156200-114170000	Weak transcription	Small Intestine	intestine
10	chr1:114158800-114168600	Weak transcription	HUVEC	blood vessel
11	chr1:114159000-114168600	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:114159000-114172200	Weak transcription	NH-A	brain
13	chr1:114159000-114173200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:114159000-114195000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:114159200-114194800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:114160400-114169800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:114160600-114168600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:114160600-114169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:114160800-114168200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:114161200-114168000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:114161400-114168600	Weak transcription	Fetal Intestine Small	intestine
22	chr1:114161600-114172400	Weak transcription	Placenta	Placenta
23	chr1:114161600-114184600	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:114161600-114184600	Weak transcription	HepG2	liver
25	chr1:114161800-114167000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:114161800-114168600	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:114161800-114199800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:114162000-114167000	Strong transcription	Liver	Liver
29	chr1:114162200-114167400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:114162200-114184600	Weak transcription	Left Ventricle	heart
31	chr1:114163200-114168800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:114163400-114168800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:114164000-114168000	Weak transcription	Psoas Muscle	Psoas
34	chr1:114164000-114168800	Weak transcription	Primary T cells from cord blood	blood
35	chr1:114164000-114168800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:114164000-114169200	Weak transcription	Fetal Kidney	kidney
37	chr1:114164000-114170400	Weak transcription	NHDF-Ad	bronchial
38	chr1:114164000-114172600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:114164200-114168000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:114164200-114169200	Weak transcription	Fetal Intestine Large	intestine
41	chr1:114165200-114166600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:114165200-114167000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:114165200-114172400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:114165400-114167000	Strong transcription	Adipose Nuclei	Adipose
45	chr1:114165400-114167000	Strong transcription	Fetal Lung	lung
46	chr1:114165600-114168800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:114166400-114166800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:114166400-114166800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:114166400-114167000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:114166400-114167000	ZNF genes & repeats	Fetal Brain Male	brain

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