Variant report

Variant	rs62179069
Chromosome Location	chr2:180139219-180139220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:180127231..180129754-chr2:180137790..180140822,6	MCF-7	breast:
2	chr2:180136977..180138919-chr2:180139042..180142671,5	MCF-7	breast:
3	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction
ENSG00000237477	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12622222	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17454087	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17454199	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17454527	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175447	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62175448	0.87[EUR][1000 genomes]
rs62175449	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62175450	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62177277	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62177280	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62177281	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177283	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177285	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177287	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177289	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177291	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62177326	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177327	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177328	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177330	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177332	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177335	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177336	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177337	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177338	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177339	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62179066	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62179067	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62179068	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180130000-180141000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:180130000-180141200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:180133600-180140200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:180133800-180141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:180134000-180139400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:180134000-180142200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:180135200-180140400	Enhancers	Brain Angular Gyrus	brain
8	chr2:180135400-180140200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:180136600-180141000	Weak transcription	Esophagus	oesophagus
10	chr2:180137000-180139600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:180137000-180140600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr2:180137200-180140000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:180137200-180141200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:180137200-180141200	Enhancers	Adipose Nuclei	Adipose
15	chr2:180137400-180140400	Enhancers	Brain Anterior Caudate	brain
16	chr2:180137400-180141200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:180137400-180141200	Enhancers	Fetal Stomach	stomach
18	chr2:180137600-180140600	Weak transcription	Stomach Mucosa	stomach
19	chr2:180137600-180141800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:180137800-180140400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:180137800-180140400	Enhancers	Osteobl	bone
22	chr2:180137800-180140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:180138000-180140400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:180138000-180140600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:180138200-180139400	Weak transcription	HSMM	muscle
26	chr2:180138200-180139800	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:180138200-180140600	Weak transcription	Fetal Intestine Large	intestine
28	chr2:180138200-180140800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:180138200-180141200	Enhancers	Hela-S3	cervix
30	chr2:180138200-180141600	Enhancers	Primary B cells from peripheral blood	blood
31	chr2:180138200-180142000	Weak transcription	NHEK	skin
32	chr2:180138400-180139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:180138400-180139600	Weak transcription	Aorta	Aorta
34	chr2:180138400-180140400	Weak transcription	Small Intestine	intestine
35	chr2:180138400-180140800	Enhancers	Colon Smooth Muscle	Colon
36	chr2:180138400-180141000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:180138600-180139400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr2:180138600-180139600	Weak transcription	HSMMtube	muscle
39	chr2:180138600-180140200	Weak transcription	A549	lung
40	chr2:180138600-180140600	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:180138600-180141800	Weak transcription	HMEC	breast
42	chr2:180138600-180154400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:180138800-180139600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr2:180138800-180139600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:180138800-180139600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:180138800-180139600	Enhancers	Placenta	Placenta
47	chr2:180138800-180139800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr2:180138800-180139800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr2:180138800-180139800	Enhancers	Brain Hippocampus Middle	brain
50	chr2:180138800-180139800	Enhancers	Lung	lung

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