Variant report

Variant	rs12958586
Chromosome Location	chr18:9718907-9718908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9716222..9719408-chr18:9720122..9723358,4	K562	blood:
2	chr18:9706129..9716760-chr18:9717289..9726025,20	K562	blood:
3	chr18:9717190..9719033-chr18:9719362..9722418,4	K562	blood:
4	chr18:9716294..9718965-chr18:9756852..9758579,2	K562	blood:
5	chr18:9717754..9719385-chr18:9828392..9830526,2	K562	blood:
6	chr18:9718684..9720358-chr18:9741067..9743489,2	MCF-7	breast:
7	chr18:9717102..9718959-chr18:9770238..9771759,2	K562	blood:

Variant related genes	Relation type
ENSG00000168461	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12326201	0.82[ASN][1000 genomes]
rs12958489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961459	0.93[ASN][1000 genomes]

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	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv469897	chr18:9674498-9870517	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv482461	chr18:9674498-9870517	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1064807	chr18:9695356-9770358	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12958586	RAB31	Cis_1M	lymphoblastoid	RTeQTL
rs12958586	RAB31	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9710000-9719600	Weak transcription	HSMM	muscle
2	chr18:9710200-9733600	Weak transcription	Left Ventricle	heart
3	chr18:9710400-9732000	Weak transcription	Fetal Stomach	stomach
4	chr18:9712400-9719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:9712400-9719000	Weak transcription	Esophagus	oesophagus
6	chr18:9712400-9719400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr18:9712400-9720200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr18:9712400-9720200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr18:9712400-9722000	Weak transcription	Aorta	Aorta
10	chr18:9712600-9719400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr18:9712600-9719600	Weak transcription	Ovary	ovary
12	chr18:9712600-9723600	Weak transcription	Fetal Muscle Leg	muscle
13	chr18:9712600-9723600	Weak transcription	Placenta	Placenta
14	chr18:9712800-9719600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr18:9712800-9720000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr18:9712800-9732000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr18:9713000-9719600	Weak transcription	Colon Smooth Muscle	Colon
18	chr18:9713200-9722200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr18:9713600-9732200	Weak transcription	Adipose Nuclei	Adipose
20	chr18:9714000-9719000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr18:9715000-9719400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr18:9715000-9719400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr18:9715000-9719800	Weak transcription	Gastric	stomach
24	chr18:9715000-9722000	Weak transcription	Spleen	Spleen
25	chr18:9715000-9723600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:9715200-9719400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr18:9715200-9719400	Weak transcription	Brain Anterior Caudate	brain
28	chr18:9715200-9719400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr18:9715200-9719800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr18:9715200-9719800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr18:9715200-9719800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr18:9715200-9719800	Weak transcription	Lung	lung
33	chr18:9715200-9723600	Weak transcription	K562	blood
34	chr18:9715400-9719400	Weak transcription	Brain Hippocampus Middle	brain
35	chr18:9716000-9719600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr18:9716200-9719000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr18:9716800-9732400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr18:9717000-9719000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:9717200-9732000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr18:9717400-9720200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr18:9717600-9719400	Weak transcription	Brain Substantia Nigra	brain
42	chr18:9717800-9721800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:9718200-9722000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr18:9718200-9732000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr18:9718200-9732600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr18:9718600-9719000	Genic enhancers	Primary monocytes fromperipheralblood	blood
47	chr18:9718600-9719000	Flanking Active TSS	Hela-S3	cervix
48	chr18:9718600-9719400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr18:9718600-9719400	Enhancers	A549	lung
50	chr18:9718600-9719400	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links