Variant report

Variant	rs10799554
Chromosome Location	chr1:224433847-224433848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10495222	0.83[ASN][1000 genomes]
rs10753461	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799539	0.83[ASN][1000 genomes]
rs10799551	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916512	0.82[ASN][1000 genomes]
rs10916515	0.81[ASN][1000 genomes]
rs10916533	0.90[ASN][1000 genomes]
rs10916534	0.85[ASN][1000 genomes]
rs10916535	0.90[ASN][1000 genomes]
rs10916543	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12134258	0.85[ASN][1000 genomes]
rs12135557	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1401318	0.90[ASN][1000 genomes]
rs1533589	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1976788	0.87[ASN][1000 genomes]
rs4654009	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4654010	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6664230	0.87[ASN][1000 genomes]
rs7522895	0.88[ASN][1000 genomes]
rs7541131	0.83[ASN][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	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
2	chr1:224407600-224434000	Weak transcription	Fetal Brain Male	brain
3	chr1:224411600-224438000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:224411600-224454400	Weak transcription	Psoas Muscle	Psoas
5	chr1:224412400-224473600	Weak transcription	HepG2	liver
6	chr1:224414200-224438000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:224415000-224436200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:224415000-224440000	Weak transcription	Fetal Kidney	kidney
9	chr1:224415600-224435000	Weak transcription	Gastric	stomach
10	chr1:224415800-224435600	Weak transcription	NHLF	lung
11	chr1:224415800-224435800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:224416000-224436600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:224416000-224465600	Weak transcription	Small Intestine	intestine
14	chr1:224417800-224435600	Weak transcription	Colonic Mucosa	Colon
15	chr1:224418000-224435400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:224418000-224436600	Weak transcription	Right Ventricle	heart
17	chr1:224418400-224439400	Weak transcription	HSMMtube	muscle
18	chr1:224419200-224435600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:224419200-224436600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:224420400-224435600	Weak transcription	HMEC	breast
21	chr1:224420800-224434400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:224423800-224439400	Weak transcription	Right Atrium	heart
23	chr1:224424000-224435400	Weak transcription	Osteobl	bone
24	chr1:224424200-224434200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:224424200-224435200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:224424200-224435400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:224424200-224435400	Weak transcription	NHEK	skin
28	chr1:224424200-224436000	Weak transcription	Fetal Lung	lung
29	chr1:224424400-224434800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:224424400-224435800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:224424600-224451600	Weak transcription	Aorta	Aorta
32	chr1:224424600-224479600	Weak transcription	Pancreas	Pancrea
33	chr1:224424800-224434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:224424800-224454200	Weak transcription	HSMM	muscle
35	chr1:224425000-224434800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:224425400-224435400	Weak transcription	Brain Germinal Matrix	brain
37	chr1:224425600-224470000	Weak transcription	NHDF-Ad	bronchial
38	chr1:224426400-224435400	Weak transcription	Brain Substantia Nigra	brain
39	chr1:224426600-224434000	Weak transcription	Liver	Liver
40	chr1:224426600-224434000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:224426600-224434200	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:224426600-224439200	Weak transcription	Spleen	Spleen
43	chr1:224427000-224435400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:224427400-224435400	Weak transcription	Ovary	ovary
45	chr1:224427600-224434000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:224427600-224434000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:224427600-224434000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:224427600-224435600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:224427600-224435800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:224427600-224436000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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