Variant report

Variant	rs4879339
Chromosome Location	chr9:27281253-27281254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10812560	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10812561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10967851	0.83[ASN][1000 genomes]
rs10967852	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967853	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10967855	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11794184	0.82[ASN][1000 genomes]
rs12342320	0.83[ASN][1000 genomes]
rs2057364	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4879337	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038108	0.94[ASN][1000 genomes]
rs7043369	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7875399	0.87[ASN][1000 genomes]
rs7876025	0.87[ASN][1000 genomes]

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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27279400-27282200	Enhancers	Brain Germinal Matrix	brain
2	chr9:27280400-27281600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:27280400-27281800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr9:27280600-27281400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr9:27280600-27281400	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr9:27280600-27281400	Enhancers	Fetal Muscle Leg	muscle
7	chr9:27280600-27281400	Enhancers	Small Intestine	intestine
8	chr9:27280600-27281600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:27280600-27281800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:27280600-27282000	Enhancers	Primary hematopoietic stem cells	blood
11	chr9:27280800-27281400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:27280800-27281400	Enhancers	Gastric	stomach
13	chr9:27280800-27281600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:27280800-27281800	Weak transcription	Lung	lung
15	chr9:27280800-27282000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:27281000-27281400	Active TSS	Brain Hippocampus Middle	brain
17	chr9:27281000-27281400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr9:27281000-27281800	Active TSS	Osteobl	bone
19	chr9:27281000-27282400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:27281000-27285600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr9:27281200-27281400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:27281200-27281400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr9:27281200-27281400	Flanking Bivalent TSS/Enh	NHEK	skin
24	chr9:27281200-27281600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:27281200-27281600	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:27281200-27281600	Enhancers	Psoas Muscle	Psoas
27	chr9:27281200-27281800	Enhancers	GM12878-XiMat	blood

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