Variant report

Variant	rs10890409
Chromosome Location	chr1:47095954-47095955
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47093097..47096139-chr1:47100393..47103970,3	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10890412	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10890413	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211334	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211339	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211340	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1139759	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026027	0.81[ASN][1000 genomes]
rs12029031	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12038572	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12048954	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12118483	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12733214	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440484	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2007344	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2218190	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275380	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3737729	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4660950	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47083000-47097200	Weak transcription	Gastric	stomach
2	chr1:47083000-47100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:47083200-47097200	Weak transcription	Primary B cells from cord blood	blood
4	chr1:47083200-47097200	Weak transcription	Aorta	Aorta
5	chr1:47083200-47097200	Weak transcription	Thymus	Thymus
6	chr1:47083200-47100200	Weak transcription	Psoas Muscle	Psoas
7	chr1:47083200-47104600	Weak transcription	Stomach Mucosa	stomach
8	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:47083400-47096800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:47083400-47097000	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:47083400-47097400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:47084800-47097000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:47085600-47099000	Weak transcription	GM12878-XiMat	blood
15	chr1:47085800-47097200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:47085800-47097600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:47087800-47097000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:47088000-47098000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:47088000-47100800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:47088200-47097000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:47088200-47097200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:47088200-47097200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:47088200-47097200	Weak transcription	NH-A	brain
24	chr1:47088200-47097400	Weak transcription	Osteobl	bone
25	chr1:47088200-47097800	Weak transcription	HSMMtube	muscle
26	chr1:47088200-47097800	Weak transcription	NHDF-Ad	bronchial
27	chr1:47088200-47098000	Weak transcription	Colonic Mucosa	Colon
28	chr1:47088200-47100000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:47088200-47100000	Weak transcription	Spleen	Spleen
30	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:47088400-47097200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:47088400-47097400	Weak transcription	NHEK	skin
33	chr1:47088400-47098000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:47088400-47098000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:47088600-47108600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:47088600-47108800	Weak transcription	Hela-S3	cervix
37	chr1:47089800-47096800	Weak transcription	Fetal Stomach	stomach
38	chr1:47089800-47112400	Weak transcription	Small Intestine	intestine
39	chr1:47090000-47096000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:47090000-47096600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:47090000-47097200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:47090000-47097200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:47090000-47097200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:47090000-47097200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:47090000-47097600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:47090200-47096600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:47090200-47097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:47090200-47097000	Weak transcription	Fetal Heart	heart
49	chr1:47090200-47097000	Weak transcription	Fetal Lung	lung
50	chr1:47090200-47097000	Weak transcription	Ovary	ovary

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