Variant report

Variant	rs400839
Chromosome Location	chr18:8660149-8660150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:8658209..8662068-chr18:8705439..8707440,3	MCF-7	breast:
2	chr18:8659422..8661406-chr18:8668712..8671092,2	K562	blood:

Variant related genes	Relation type
ENSG00000168502	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17479191	0.88[ASN][1000 genomes]
rs392603	0.90[CHB][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs4798668	0.87[ASN][1000 genomes]
rs529984	0.86[ASN][1000 genomes]
rs538700	0.86[ASN][1000 genomes]
rs601126	0.86[ASN][1000 genomes]
rs62086810	0.82[ASN][1000 genomes]
rs62086811	0.83[ASN][1000 genomes]
rs9675533	0.86[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	nsv2200	chr18:8618182-8663130	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs400839	SLMO1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8653800-8703400	Weak transcription	Right Atrium	heart
2	chr18:8655200-8660600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr18:8655200-8662400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr18:8655400-8662000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:8657000-8660800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr18:8657200-8661600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr18:8657400-8661800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:8657800-8662000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr18:8658000-8661600	Weak transcription	Brain Angular Gyrus	brain
10	chr18:8658000-8661600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr18:8658200-8660200	Weak transcription	NH-A	brain
12	chr18:8658200-8660600	Weak transcription	NHLF	lung
13	chr18:8658200-8661000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr18:8658200-8661200	Weak transcription	NHDF-Ad	bronchial
15	chr18:8658200-8661400	Weak transcription	Fetal Brain Female	brain
16	chr18:8658200-8661800	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:8658200-8661800	Weak transcription	Brain Substantia Nigra	brain
18	chr18:8658200-8661800	Weak transcription	HMEC	breast
19	chr18:8658400-8660800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:8658400-8661200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr18:8658400-8661600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr18:8658400-8661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr18:8658400-8661600	Weak transcription	Hela-S3	cervix
24	chr18:8658400-8661600	Weak transcription	HSMMtube	muscle
25	chr18:8658400-8661800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr18:8658400-8665200	Weak transcription	A549	lung
27	chr18:8658600-8661400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr18:8659000-8660600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr18:8659000-8661000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr18:8659000-8663800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:8659200-8660200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
32	chr18:8659200-8660200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr18:8659200-8661200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr18:8659200-8661400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr18:8659200-8661800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr18:8659400-8660400	Enhancers	K562	blood
37	chr18:8659400-8661000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr18:8659400-8661400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr18:8659800-8660400	Weak transcription	Brain Germinal Matrix	brain
40	chr18:8659800-8661000	Weak transcription	Fetal Brain Male	brain
41	chr18:8660000-8660200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr18:8660000-8660400	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links