Variant report

Variant	rs13394908
Chromosome Location	chr2:180138820-180138821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180127231..180129754-chr2:180137790..180140822,6	MCF-7	breast:
2	chr2:180127590..180133149-chr2:180134052..180141026,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLEKHA3-7	chr2:180138558-180138855	XLOC_001771

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10173853	1.00[AMR][1000 genomes]
rs10176828	1.00[AMR][1000 genomes]
rs10178559	1.00[AMR][1000 genomes]
rs10186707	1.00[AMR][1000 genomes]
rs10205588	1.00[AMR][1000 genomes]
rs10207754	1.00[AMR][1000 genomes]
rs10208882	1.00[AMR][1000 genomes]
rs10221811	1.00[AMR][1000 genomes]
rs12328593	1.00[AMR][1000 genomes]
rs12611473	1.00[AMR][1000 genomes]
rs12613089	1.00[AMR][1000 genomes]
rs12616452	1.00[AMR][1000 genomes]
rs12622434	1.00[AMR][1000 genomes]
rs13382573	1.00[AMR][1000 genomes]
rs13391187	1.00[AMR][1000 genomes]
rs13395559	1.00[AMR][1000 genomes]
rs13408774	1.00[AMR][1000 genomes]
rs13412820	1.00[AMR][1000 genomes]
rs13417112	1.00[AMR][1000 genomes]
rs13422693	1.00[AMR][1000 genomes]
rs13429191	1.00[AMR][1000 genomes]
rs16866630	1.00[AMR][1000 genomes]
rs28508327	1.00[AMR][1000 genomes]
rs35041512	1.00[AMR][1000 genomes]
rs7581898	1.00[AMR][1000 genomes]
rs7588135	1.00[AMR][1000 genomes]
rs7601965	1.00[AMR][1000 genomes]
rs9288024	1.00[AMR][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:59 , 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	chr2:180130400-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:180133600-180140200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:180133800-180139200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:180133800-180141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:180134000-180139400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:180134000-180142200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:180135200-180140400	Enhancers	Brain Angular Gyrus	brain
10	chr2:180135400-180140200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:180136600-180141000	Weak transcription	Esophagus	oesophagus
12	chr2:180137000-180139000	Flanking Active TSS	HepG2	liver
13	chr2:180137000-180139600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:180137000-180140600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:180137200-180140000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr2:180137200-180141200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:180137200-180141200	Enhancers	Adipose Nuclei	Adipose
18	chr2:180137400-180140400	Enhancers	Brain Anterior Caudate	brain
19	chr2:180137400-180141200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:180137400-180141200	Enhancers	Fetal Stomach	stomach
21	chr2:180137600-180140600	Weak transcription	Stomach Mucosa	stomach
22	chr2:180137600-180141800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:180137800-180139200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:180137800-180140400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:180137800-180140400	Enhancers	Osteobl	bone
26	chr2:180137800-180140600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:180138000-180140400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:180138000-180140600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:180138200-180139400	Weak transcription	HSMM	muscle
30	chr2:180138200-180139800	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:180138200-180140600	Weak transcription	Fetal Intestine Large	intestine
32	chr2:180138200-180140800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:180138200-180141200	Enhancers	Hela-S3	cervix
34	chr2:180138200-180141600	Enhancers	Primary B cells from peripheral blood	blood
35	chr2:180138200-180142000	Weak transcription	NHEK	skin
36	chr2:180138400-180139000	Enhancers	Primary B cells from cord blood	blood
37	chr2:180138400-180139400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:180138400-180139600	Weak transcription	Aorta	Aorta
39	chr2:180138400-180140400	Weak transcription	Small Intestine	intestine
40	chr2:180138400-180140800	Enhancers	Colon Smooth Muscle	Colon
41	chr2:180138400-180141000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:180138600-180139400	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr2:180138600-180139600	Weak transcription	HSMMtube	muscle
44	chr2:180138600-180140200	Weak transcription	A549	lung
45	chr2:180138600-180140600	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:180138600-180141800	Weak transcription	HMEC	breast
47	chr2:180138600-180154400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:180138800-180139600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr2:180138800-180139600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:180138800-180139600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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