Variant report

Variant	rs66773232
Chromosome Location	chr2:54201107-54201108
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54198564..54201435-chr2:54359737..54361960,2	K562	blood:
2	chr2:54074773..54076424-chr2:54200661..54203380,2	MCF-7	breast:
3	chr2:54196644..54199025-chr2:54199864..54201525,2	MCF-7	breast:
4	chr2:54157567..54166967-chr2:54194910..54201681,12	MCF-7	breast:
5	chr2:54200308..54201995-chr2:54341624..54344504,2	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000265452	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10084374	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10167891	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10168293	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10181999	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10183655	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10186566	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11674724	0.87[ASN][1000 genomes]
rs11683741	0.92[ASN][1000 genomes]
rs11689025	0.95[ASN][1000 genomes]
rs11694711	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11893270	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13394278	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477258	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045452	0.96[ASN][1000 genomes]
rs2112122	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28653587	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28851028	0.83[ASN][1000 genomes]
rs2909459	0.93[ASN][1000 genomes]
rs2949815	0.91[ASN][1000 genomes]
rs3731967	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671742	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671746	0.86[ASN][1000 genomes]
rs4671747	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55692047	0.89[ASN][1000 genomes]
rs56302494	0.87[ASN][1000 genomes]
rs62139336	0.96[ASN][1000 genomes]
rs6545377	0.89[ASN][1000 genomes]
rs6545380	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6711105	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6711217	0.83[EUR][1000 genomes]
rs6714450	0.81[ASN][1000 genomes]
rs6715488	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742042	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6743455	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746965	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6748976	0.88[ASN][1000 genomes]
rs6748997	0.86[ASN][1000 genomes]
rs72799298	0.88[ASN][1000 genomes]
rs72904908	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7559947	0.96[ASN][1000 genomes]
rs7564912	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7591431	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs805310	0.93[ASN][1000 genomes]
rs805344	0.93[ASN][1000 genomes]
rs805416	0.83[AMR][1000 genomes]
rs805448	0.81[AMR][1000 genomes]
rs9631059	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54198600-54209000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54198600-54212000	Weak transcription	Spleen	Spleen
3	chr2:54198800-54202600	Weak transcription	Lung	lung
4	chr2:54198800-54204200	Weak transcription	Esophagus	oesophagus
5	chr2:54198800-54205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54199000-54201200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:54199000-54203200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:54199000-54203400	Weak transcription	Left Ventricle	heart
9	chr2:54199000-54203400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:54199000-54204200	Weak transcription	Thymus	Thymus
11	chr2:54199000-54207200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:54199000-54208600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:54199000-54214200	Weak transcription	Stomach Mucosa	stomach
14	chr2:54199000-54214400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:54199000-54215600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:54199000-54221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
18	chr2:54199200-54201200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:54199200-54201200	Weak transcription	Ovary	ovary
20	chr2:54199200-54201400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:54199200-54201400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:54199200-54201400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:54199200-54201400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:54199200-54201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:54199200-54201400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:54199200-54201400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:54199200-54201400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:54199200-54201400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:54199200-54201400	Weak transcription	Adipose Nuclei	Adipose
30	chr2:54199200-54201400	Weak transcription	Liver	Liver
31	chr2:54199200-54201400	Weak transcription	Brain Angular Gyrus	brain
32	chr2:54199200-54201400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:54199200-54201400	Weak transcription	Fetal Lung	lung
34	chr2:54199200-54201400	Weak transcription	Fetal Thymus	thymus
35	chr2:54199200-54201400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:54199200-54201400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:54199200-54201400	Weak transcription	Osteobl	bone
38	chr2:54199200-54201600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr2:54199200-54201800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:54199200-54201800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:54199200-54202000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:54199200-54202000	Weak transcription	NHLF	lung
43	chr2:54199200-54202200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:54199200-54202200	Weak transcription	Fetal Intestine Small	intestine
45	chr2:54199200-54202800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:54199200-54204200	Weak transcription	Pancreas	Pancrea
47	chr2:54199200-54204400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:54199200-54204400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:54199200-54205600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr2:54199200-54206000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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