Variant report

Variant	rs12457728
Chromosome Location	chr18:9733359-9733360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9705672..9708161-chr18:9732147..9734468,2	K562	blood:
2	chr18:9728140..9730225-chr18:9731691..9733980,2	MCF-7	breast:
3	chr18:9729801..9734726-chr18:9735904..9739407,5	K562	blood:
4	chr18:9732492..9734472-chr18:9738392..9739946,2	MCF-7	breast:
5	chr18:9727087..9729613-chr18:9731693..9733539,2	MCF-7	breast:
6	chr18:9705049..9708161-chr18:9732147..9734824,4	K562	blood:
7	chr18:9733101..9737818-chr18:9912631..9916013,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101558	Chromatin interaction
ENSG00000272799	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs34735184	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62078924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6506685	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7230946	0.82[EUR][1000 genomes]
rs8087451	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs921837	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv3393081	chr18:9731352-9734450	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12457728	RAB31	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9710200-9733600	Weak transcription	Left Ventricle	heart
2	chr18:9719800-9733600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr18:9719800-9734400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:9720000-9737400	Weak transcription	Brain Anterior Caudate	brain
5	chr18:9720000-9742000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:9720600-9733600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr18:9720600-9734200	Weak transcription	HUVEC	blood vessel
8	chr18:9720800-9737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:9721000-9741600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:9721200-9737200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr18:9721800-9737600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr18:9722400-9733400	Weak transcription	Right Ventricle	heart
13	chr18:9722400-9734400	Weak transcription	Colonic Mucosa	Colon
14	chr18:9723800-9734200	Weak transcription	Fetal Lung	lung
15	chr18:9724000-9737200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr18:9725000-9737600	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:9725600-9733600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:9726200-9734200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr18:9727200-9733600	Weak transcription	Esophagus	oesophagus
20	chr18:9730800-9733600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr18:9731000-9733600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr18:9731000-9734200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr18:9731200-9733600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr18:9731200-9734000	Weak transcription	Liver	Liver
25	chr18:9731400-9733600	Weak transcription	NHLF	lung
26	chr18:9731400-9734200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:9731400-9734400	Weak transcription	Thymus	Thymus
28	chr18:9731400-9737200	Weak transcription	HSMM	muscle
29	chr18:9731600-9733400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:9731600-9736400	Weak transcription	HMEC	breast
31	chr18:9732000-9733400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:9732000-9733600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr18:9732000-9733600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr18:9732000-9733800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
35	chr18:9732000-9733800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr18:9732000-9733800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr18:9732000-9733800	Genic enhancers	Hela-S3	cervix
38	chr18:9732000-9733800	Strong transcription	NHEK	skin
39	chr18:9732000-9734000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr18:9732000-9734200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
41	chr18:9732000-9735800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:9732000-9736000	Strong transcription	Fetal Stomach	stomach
43	chr18:9732000-9736200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr18:9732000-9736600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr18:9732000-9737000	Weak transcription	NH-A	brain
46	chr18:9732200-9733400	Strong transcription	Osteobl	bone
47	chr18:9732200-9733600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr18:9732200-9733800	Strong transcription	Fetal Muscle Leg	muscle
49	chr18:9732200-9733800	Strong transcription	HSMMtube	muscle
50	chr18:9732200-9734000	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links