Variant report

Variant	rs1864538
Chromosome Location	chr2:10147915-10147916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10146994..10149729-chr2:10182824..10184485,2	MCF-7	breast:
2	chr2:10147171..10148722-chr2:10150073..10151791,3	K562	blood:
3	chr2:10147491..10150465-chr2:10152525..10155691,3	MCF-7	breast:
4	chr2:10147901..10149984-chr2:10215589..10217531,2	K562	blood:

Variant related genes	Relation type
ENSG00000172059	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10179034	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203214	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203322	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052835	0.96[ASN][1000 genomes]
rs1052838	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11246	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13385356	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13394227	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1465638	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1594398	0.98[ASN][1000 genomes]
rs1594399	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16867280	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864537	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2099204	0.84[AMR][1000 genomes]
rs2163338	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791749	0.95[ASN][1000 genomes]
rs3791750	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4668661	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669515	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669516	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6705493	0.83[AMR][1000 genomes]
rs6720380	0.83[AMR][1000 genomes]
rs6720387	0.83[AMR][1000 genomes]
rs6733635	0.83[AMR][1000 genomes]
rs6751681	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7596286	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs930137	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs934303	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][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	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
3	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
4	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:10131600-10149600	Weak transcription	Brain Substantia Nigra	brain
6	chr2:10134800-10150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:10137000-10148000	Weak transcription	Hela-S3	cervix
8	chr2:10137600-10149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:10139800-10150400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:10141600-10160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:10142400-10148200	Enhancers	Adipose Nuclei	Adipose
12	chr2:10142800-10148000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:10145800-10151000	Enhancers	Pancreas	Pancrea
14	chr2:10146400-10148000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:10146400-10148800	Enhancers	Liver	Liver
16	chr2:10146400-10148800	Enhancers	Gastric	stomach
17	chr2:10146400-10150800	Enhancers	Colon Smooth Muscle	Colon
18	chr2:10146400-10150800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr2:10146400-10151200	Enhancers	Placenta	Placenta
20	chr2:10146600-10148800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr2:10146600-10148800	Enhancers	Right Atrium	heart
22	chr2:10146800-10148400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr2:10146800-10148800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr2:10146800-10150200	Enhancers	Rectal Smooth Muscle	rectum
25	chr2:10146800-10150800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr2:10146800-10150800	Enhancers	HSMM	muscle
27	chr2:10146800-10151000	Enhancers	NHDF-Ad	bronchial
28	chr2:10146800-10151200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:10147000-10148000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:10147000-10148200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:10147000-10148400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:10147000-10148400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:10147000-10148800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:10147000-10150600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:10147000-10150800	Enhancers	HSMMtube	muscle
36	chr2:10147200-10148200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:10147200-10148200	Weak transcription	Ovary	ovary
38	chr2:10147200-10148400	Weak transcription	Right Ventricle	heart
39	chr2:10147200-10148400	Weak transcription	NH-A	brain
40	chr2:10147200-10148600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:10147200-10148600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:10147200-10148600	Enhancers	Osteobl	bone
43	chr2:10147200-10149000	Weak transcription	Small Intestine	intestine
44	chr2:10147200-10149400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:10147200-10149400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:10147200-10149800	Enhancers	Stomach Smooth Muscle	stomach
47	chr2:10147200-10150600	Weak transcription	Esophagus	oesophagus
48	chr2:10147200-10150800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:10147200-10151200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:10147400-10148200	Weak transcription	Lung	lung

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