Variant report

Variant	rs10890413
Chromosome Location	chr1:47177684-47177685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47141770..47144692-chr1:47177130..47178944,2	K562	blood:
2	chr1:47167694..47169718-chr1:47177678..47180403,2	MCF-7	breast:
3	chr1:47174939..47178626-chr1:47183441..47185833,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10890409	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10890412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211334	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211339	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211340	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211351	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1139759	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12026027	0.86[ASN][1000 genomes]
rs12029031	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038572	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048954	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12118483	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12138338	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12142631	0.82[EUR][1000 genomes]
rs12733214	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1440484	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007344	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2218190	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275380	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3737729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660950	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4660957	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:47160600-47181200	Strong transcription	Dnd41	blood
5	chr1:47160800-47181800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:47160800-47182200	Strong transcription	Primary B cells from cord blood	blood
7	chr1:47160800-47182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:47160800-47182400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:47160800-47182600	Strong transcription	Placenta	Placenta
10	chr1:47161200-47182200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:47161400-47182200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:47161400-47182800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:47164400-47182200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:47164400-47182800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:47164600-47181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:47165600-47182200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:47166200-47182400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:47166600-47182400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:47166600-47182400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:47166600-47182800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:47166600-47182800	Strong transcription	Fetal Thymus	thymus
22	chr1:47166800-47181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:47166800-47182200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:47166800-47182400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:47166800-47182600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:47166800-47182800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:47167000-47182400	Strong transcription	Fetal Muscle Leg	muscle
28	chr1:47167000-47182800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:47167200-47180800	Strong transcription	NHEK	skin
30	chr1:47167200-47182600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:47167400-47182000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:47167600-47183400	Weak transcription	Aorta	Aorta
33	chr1:47168400-47180600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:47168600-47180800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:47170800-47180600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:47171000-47180600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:47171200-47182400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr1:47171400-47178200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:47172000-47181400	Strong transcription	HSMM	muscle
40	chr1:47172200-47183800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:47172400-47180800	Weak transcription	Esophagus	oesophagus
42	chr1:47172600-47179400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:47172800-47178800	Weak transcription	NHLF	lung
44	chr1:47172800-47179800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:47172800-47180200	Weak transcription	Pancreas	Pancrea
46	chr1:47172800-47181200	Weak transcription	Right Ventricle	heart
47	chr1:47173000-47178800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:47173000-47180800	Weak transcription	Hela-S3	cervix
49	chr1:47173000-47182400	Weak transcription	Small Intestine	intestine
50	chr1:47173200-47179200	Weak transcription	HepG2	liver

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