Variant report

Variant	rs12089658
Chromosome Location	chr1:151117010-151117011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151112727..151117017-chr1:151118116..151120270,3	K562	blood:
2	chr1:151096194..151098701-chr1:151116242..151118774,2	MCF-7	breast:
3	chr1:151114895..151122057-chr1:151125026..151130825,9	MCF-7	breast:
4	chr1:151008899..151010447-chr1:151116259..151119248,2	MCF-7	breast:
5	chr1:151115125..151117967-chr1:151253558..151255357,2	K562	blood:
6	chr1:151109028..151112291-chr1:151113939..151118222,5	K562	blood:
7	chr1:151112451..151114594-chr1:151115769..151118069,3	K562	blood:
8	chr1:151114749..151117567-chr1:151151983..151153922,2	K562	blood:
9	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:
10	chr1:151112451..151114462-chr1:151116329..151118583,3	K562	blood:
11	chr1:151116657..151121305-chr1:151127749..151129795,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163141	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11204774	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs12058128	0.84[EUR][1000 genomes]
rs12060682	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12067174	0.82[ASW][hapmap]
rs12068365	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs12074309	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs12078857	1.00[ASW][hapmap]
rs12088941	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12090246	0.82[ASW][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs12097169	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16832976	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs3892218	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59603391	0.90[EUR][1000 genomes]
rs61321900	0.98[EUR][1000 genomes]
rs6664387	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs7526955	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs955955	0.82[ASW][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12089658	LYSMD1	cis	cerebellar cortex	BrainEAC
rs12089658	LYSMD1	cis	brain	BrainEAC

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
2	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
4	chr1:151105600-151118000	Weak transcription	Gastric	stomach
5	chr1:151105800-151117200	Weak transcription	Spleen	Spleen
6	chr1:151107000-151117600	Weak transcription	Colonic Mucosa	Colon
7	chr1:151108400-151117200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:151108600-151117800	Weak transcription	Esophagus	oesophagus
9	chr1:151109600-151117600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:151110200-151117600	Weak transcription	Pancreas	Pancrea
11	chr1:151112800-151117400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:151113000-151118000	Weak transcription	Liver	Liver
13	chr1:151114800-151117200	Enhancers	Left Ventricle	heart
14	chr1:151114800-151117200	Enhancers	Right Ventricle	heart
15	chr1:151114800-151117400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:151114800-151117400	Enhancers	Psoas Muscle	Psoas
17	chr1:151114800-151117600	Enhancers	HSMM	muscle
18	chr1:151114800-151117800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:151115000-151118200	Enhancers	K562	blood
20	chr1:151115000-151118600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr1:151115200-151117200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:151115200-151117200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:151115400-151117400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:151115400-151117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:151115400-151117400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr1:151115400-151117400	Genic enhancers	Fetal Stomach	stomach
27	chr1:151115400-151117600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:151115600-151117200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:151115600-151117200	Enhancers	Adipose Nuclei	Adipose
30	chr1:151115600-151117200	Enhancers	Fetal Thymus	thymus
31	chr1:151115600-151117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:151115600-151117400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:151115600-151117400	Enhancers	Fetal Lung	lung
34	chr1:151115600-151118000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:151115600-151118800	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr1:151115800-151117200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:151115800-151117200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr1:151115800-151117200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:151115800-151117400	Enhancers	Colon Smooth Muscle	Colon
40	chr1:151115800-151117400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:151116000-151117400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:151116000-151117600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:151116000-151117600	Weak transcription	Thymus	Thymus
44	chr1:151116200-151117200	Enhancers	Brain Hippocampus Middle	brain
45	chr1:151116200-151117200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
46	chr1:151116400-151117200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:151116400-151117400	Flanking Active TSS	Fetal Brain Female	brain
48	chr1:151116400-151117400	Enhancers	Ovary	ovary
49	chr1:151116400-151117800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:151116400-151118800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links