Variant report

Variant	rs12343358
Chromosome Location	chr9:27281151-27281152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10967838	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10967851	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10967855	0.83[JPT][hapmap]
rs10967856	0.83[JPT][hapmap]
rs10967860	0.83[ASW][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap]
rs10967861	0.91[ASW][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap]
rs11794184	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12342320	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13288748	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3739534	0.91[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs3739538	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3739539	0.91[JPT][hapmap]
rs3739541	0.91[JPT][hapmap]
rs7038108	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7875391	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7875399	0.87[JPT][hapmap];0.80[LWK][hapmap];0.84[MKK][hapmap]
rs7875778	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7876025	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv892864	chr9:27176554-27296705	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1018864	chr9:27195840-27294815	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2761268	chr9:27195852-27291261	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv466336	chr9:27196119-27292703	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471294	chr9:27196119-27292703	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv613947	chr9:27196119-27292703	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1018258	chr9:27234184-27292709	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1019688	chr9:27234184-27356374	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv466337	chr9:27250868-27353460	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv613949	chr9:27250868-27353460	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv892866	chr9:27274370-27332818	Bivalent Enhancer Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv525488	chr9:27281151-27283020	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27276800-27281200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr9:27279400-27282200	Enhancers	Brain Germinal Matrix	brain
3	chr9:27280400-27281600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:27280400-27281800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr9:27280600-27281200	Enhancers	Ovary	ovary
6	chr9:27280600-27281400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr9:27280600-27281400	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr9:27280600-27281400	Enhancers	Fetal Muscle Leg	muscle
9	chr9:27280600-27281400	Enhancers	Small Intestine	intestine
10	chr9:27280600-27281600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:27280600-27281800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr9:27280600-27282000	Enhancers	Primary hematopoietic stem cells	blood
13	chr9:27280800-27281400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:27280800-27281400	Enhancers	Gastric	stomach
15	chr9:27280800-27281600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:27280800-27281800	Weak transcription	Lung	lung
17	chr9:27280800-27282000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:27281000-27281200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:27281000-27281200	Weak transcription	Psoas Muscle	Psoas
20	chr9:27281000-27281400	Active TSS	Brain Hippocampus Middle	brain
21	chr9:27281000-27281400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr9:27281000-27281800	Active TSS	Osteobl	bone
23	chr9:27281000-27282400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:27281000-27285600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links