Variant report

Variant	rs10890387
Chromosome Location	chr1:46753027-46753028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46752392..46755231-chr1:46809649..46812532,2	K562	blood:
2	chr1:46751120..46753625-chr1:46758449..46761114,3	MCF-7	breast:
3	chr1:46712253..46715558-chr1:46749979..46754633,4	K562	blood:
4	chr1:46750645..46754221-chr1:46805121..46809477,5	K562	blood:
5	chr1:46750679..46754864-chr1:46805103..46809181,6	K562	blood:

Variant related genes	Relation type
ENSG00000117481	Chromatin interaction
ENSG00000085999	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10789488	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10890386	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10890388	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11584233	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11586229	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12039667	0.83[AMR][1000 genomes]
rs12044708	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12125573	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1547180	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2093044	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4660918	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4660919	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4660920	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660921	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6429596	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7527133	0.88[AMR][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	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers 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	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 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	chr1:46714400-46754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:46715200-46764200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:46715400-46754200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:46715400-46763800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:46715400-46764400	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:46715400-46765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:46720800-46766400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:46721600-46753800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:46723200-46755200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:46724200-46756000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:46730000-46764000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:46733600-46766200	Weak transcription	Small Intestine	intestine
13	chr1:46740400-46753800	Strong transcription	NH-A	brain
14	chr1:46741200-46755000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:46741600-46763400	Strong transcription	Fetal Stomach	stomach
16	chr1:46742000-46753800	Strong transcription	Brain Germinal Matrix	brain
17	chr1:46742200-46754400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:46742600-46756000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:46742800-46753800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:46742800-46753800	Strong transcription	NHEK	skin
21	chr1:46742800-46756200	Strong transcription	Placenta	Placenta
22	chr1:46743200-46756000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:46743200-46756200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr1:46743200-46763600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:46743400-46753800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:46743400-46756000	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr1:46743400-46764000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:46743400-46764000	Strong transcription	Liver	Liver
29	chr1:46743600-46763800	Strong transcription	Fetal Lung	lung
30	chr1:46744600-46761400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:46744800-46753800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:46745200-46766400	Weak transcription	Stomach Mucosa	stomach
33	chr1:46748800-46756000	Strong transcription	Adipose Nuclei	Adipose
34	chr1:46748800-46756000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr1:46749000-46755000	Strong transcription	Brain Anterior Caudate	brain
36	chr1:46749400-46756400	Strong transcription	Fetal Brain Female	brain
37	chr1:46749600-46755000	Genic enhancers	K562	blood
38	chr1:46749600-46755800	Strong transcription	Brain Angular Gyrus	brain
39	chr1:46749800-46753800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:46749800-46756000	Strong transcription	Brain Hippocampus Middle	brain
41	chr1:46749800-46756200	Strong transcription	HepG2	liver
42	chr1:46750400-46754800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr1:46750600-46754600	Strong transcription	Ovary	ovary
44	chr1:46750600-46756400	Strong transcription	Fetal Intestine Large	intestine
45	chr1:46750600-46762400	Weak transcription	Fetal Brain Male	brain
46	chr1:46750800-46753200	Weak transcription	Fetal Kidney	kidney
47	chr1:46750800-46764200	Weak transcription	Right Atrium	heart
48	chr1:46751000-46753600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:46751000-46753800	Strong transcription	Osteobl	bone
50	chr1:46751000-46756000	Strong transcription	Left Ventricle	heart

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