Variant report

Variant	rs926408
Chromosome Location	chr6:149552587-149552588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149351996..149353852-chr6:149550968..149553135,2	MCF-7	breast:
2	chr6:149550516..149553121-chr6:149563876..149565392,2	MCF-7	breast:
3	chr6:149549830..149552790-chr6:149637558..149640199,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction
ENSG00000225924	Chromatin interaction
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13203475	0.81[JPT][hapmap]
rs9498262	0.83[CHB][hapmap];0.82[GIH][hapmap];0.81[EUR][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	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs926408	LATS1	cis	parietal	SCAN
rs926408	RAET1L	cis	parietal	SCAN
rs926408	RAET1L	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149542200-149560600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:149545400-149553000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:149545800-149553000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:149545800-149557800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:149545800-149560200	Weak transcription	Right Atrium	heart
6	chr6:149546800-149556200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:149549600-149553000	Weak transcription	Fetal Thymus	thymus
8	chr6:149549600-149554000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:149549600-149557200	Weak transcription	Fetal Stomach	stomach
10	chr6:149549800-149552800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:149549800-149553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:149549800-149553600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:149550000-149552600	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:149550000-149554000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:149550000-149556000	Enhancers	Brain Hippocampus Middle	brain
16	chr6:149550200-149553000	Weak transcription	Fetal Heart	heart
17	chr6:149550200-149553600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:149550200-149554000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:149550200-149554200	Enhancers	Brain Anterior Caudate	brain
20	chr6:149550200-149554200	Weak transcription	HSMMtube	muscle
21	chr6:149550200-149557800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:149550400-149553000	Enhancers	Brain Substantia Nigra	brain
23	chr6:149550400-149554600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:149550600-149553000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:149550800-149553200	Weak transcription	Placenta	Placenta
26	chr6:149551000-149554000	Weak transcription	Pancreas	Pancrea
27	chr6:149551000-149555800	Weak transcription	Brain Germinal Matrix	brain
28	chr6:149551000-149557600	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr6:149551200-149554800	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:149551400-149554600	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:149551600-149554000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr6:149551600-149554000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:149551600-149554600	Enhancers	Primary B cells from cord blood	blood
34	chr6:149551600-149556400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:149551800-149552600	Enhancers	Duodenum Mucosa	Duodenum
36	chr6:149551800-149553600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr6:149551800-149558000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:149552000-149553800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:149552000-149556400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:149552200-149552800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr6:149552200-149553400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr6:149552200-149553800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr6:149552200-149554000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:149552200-149555600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:149552200-149555600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:149552400-149552600	Enhancers	HMEC	breast
47	chr6:149552400-149553400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:149552400-149553400	Weak transcription	Ovary	ovary
49	chr6:149552400-149553600	Weak transcription	Hela-S3	cervix
50	chr6:149552400-149554800	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links