Variant report

Variant	rs1540292
Chromosome Location	chr22:34304073-34304074
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	chr22:34300595..34304253-chr22:34306616..34309764,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2157153	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2267314	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2267319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35759081	1.00[ASN][1000 genomes]
rs5754752	0.81[CHD][hapmap]
rs5999134	0.95[ASN][1000 genomes]
rs5999143	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61356969	0.98[ASN][1000 genomes]
rs7287395	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1066419	chr22:34231732-34553006	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv544690	chr22:34231732-34553006	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3343210	chr22:34236744-34404210	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv588938	chr22:34270568-34307875	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1540292	RBM9	cis	cerebellum	SCAN
rs1540292	LIMK2	cis	parietal	SCAN
rs1540292	SLC5A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34291000-34304200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr22:34291200-34304200	Weak transcription	Brain Anterior Caudate	brain
3	chr22:34291200-34312800	Weak transcription	HepG2	liver
4	chr22:34291800-34305000	Weak transcription	Fetal Intestine Small	intestine
5	chr22:34291800-34313800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:34293800-34306200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr22:34293800-34315000	Weak transcription	Pancreas	Pancrea
8	chr22:34294200-34310400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr22:34296000-34304800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr22:34296000-34304800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr22:34296400-34304800	Weak transcription	Brain Hippocampus Middle	brain
12	chr22:34296600-34313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr22:34296800-34304200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr22:34297400-34304400	Weak transcription	Brain Angular Gyrus	brain
15	chr22:34297400-34305200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr22:34297400-34313800	Weak transcription	Gastric	stomach
17	chr22:34297800-34304200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr22:34298200-34305800	Weak transcription	Adipose Nuclei	Adipose
19	chr22:34298400-34307000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr22:34298600-34306600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr22:34298600-34306800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr22:34298800-34304200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr22:34298800-34310000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr22:34299200-34304200	Weak transcription	Ovary	ovary
25	chr22:34301400-34304200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:34301400-34304800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:34302200-34304800	Weak transcription	Stomach Mucosa	stomach
28	chr22:34302800-34306200	Enhancers	Fetal Heart	heart
29	chr22:34303000-34304200	Enhancers	Colon Smooth Muscle	Colon
30	chr22:34303000-34304600	Enhancers	Primary B cells from peripheral blood	blood
31	chr22:34303000-34306400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr22:34303200-34304200	Weak transcription	Aorta	Aorta
33	chr22:34303200-34306600	Enhancers	Left Ventricle	heart
34	chr22:34303400-34304400	Weak transcription	Fetal Kidney	kidney
35	chr22:34303400-34305400	Weak transcription	Right Atrium	heart
36	chr22:34303400-34307600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:34303600-34304400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr22:34303800-34304400	Enhancers	Lung	lung
39	chr22:34303800-34304600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr22:34303800-34305200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr22:34303800-34314000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr22:34304000-34304200	Enhancers	Fetal Brain Female	brain
43	chr22:34304000-34304200	ZNF genes & repeats	GM12878-XiMat	blood
44	chr22:34304000-34304400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr22:34304000-34304400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr22:34304000-34304800	Enhancers	Rectal Smooth Muscle	rectum
47	chr22:34304000-34305000	Weak transcription	Right Ventricle	heart
48	chr22:34304000-34305400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr22:34304000-34305600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr22:34304000-34306200	Enhancers	Fetal Stomach	stomach

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