Variant report

Variant	rs2168987
Chromosome Location	chr4:120043874-120043875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120033457..120035928-chr4:120042450..120044760,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10010982	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10011203	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10022764	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10033187	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10518310	0.80[CEU][hapmap];0.86[GIH][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13125695	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459059	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459060	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1459061	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1459062	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1809262	0.95[ASN][1000 genomes]
rs2389727	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389728	0.85[CEU][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34183945	0.83[ASN][1000 genomes]
rs4834746	0.81[AMR][1000 genomes]
rs4834750	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4834751	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534125	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534126	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534127	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534128	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68066537	0.84[ASN][1000 genomes]
rs6817570	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs718280	0.82[ASN][1000 genomes]
rs7669449	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7669518	0.81[AMR][1000 genomes]
rs898170	0.98[ASN][1000 genomes]
rs9307468	0.88[EUR][1000 genomes];0.97[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1007214	chr4:120007913-120112460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv1003827	chr4:120008227-120112460	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv522386	chr4:120009147-120115379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
9	nsv1007619	chr4:120014898-120112460	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2168987	SYNPO2	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120014800-120045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:120034400-120044800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:120037000-120046600	Weak transcription	Right Ventricle	heart
4	chr4:120038600-120044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:120038600-120045000	Weak transcription	Aorta	Aorta
6	chr4:120038800-120045600	Weak transcription	Adipose Nuclei	Adipose
7	chr4:120039800-120044800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:120039800-120044800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:120039800-120044800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:120039800-120045000	Weak transcription	NHDF-Ad	bronchial
11	chr4:120040000-120044800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:120040000-120045400	Weak transcription	Osteobl	bone
13	chr4:120040600-120044800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:120040600-120045800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:120040800-120044400	Weak transcription	HUVEC	blood vessel
16	chr4:120041200-120052600	Weak transcription	Left Ventricle	heart
17	chr4:120041800-120044000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:120041800-120044400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:120043400-120045800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:120043800-120044000	Enhancers	HSMM	muscle
21	chr4:120043800-120044600	Weak transcription	Muscle Satellite Cultured Cells	--

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