Variant report

Variant	rs2025272
Chromosome Location	chr6:164089576-164089577
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:164081712..164084743-chr6:164086465..164089589,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10455926	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191767	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216163	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234977	1.00[CHB][hapmap]
rs1744929	1.00[CHB][hapmap]
rs2321849	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2321850	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709737	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709739	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455913	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902395	1.00[CHB][hapmap]
rs71569414	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744302	1.00[CHB][hapmap]
rs7754222	1.00[CHB][hapmap]
rs7764847	1.00[CHB][hapmap]
rs7767021	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767804	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347765	1.00[CHB][hapmap]
rs9365575	1.00[CHB][hapmap]
rs9458843	1.00[CHB][hapmap]
rs9458860	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2758092	chr6:163992064-164161903	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2759490	chr6:163992064-164161903	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1019107	chr6:164056423-164144164	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2025272	SFT2D1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164057200-164092400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:164085600-164092000	Enhancers	Brain Germinal Matrix	brain
3	chr6:164086200-164092800	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:164086400-164091000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:164086800-164089600	Enhancers	Fetal Brain Male	brain
6	chr6:164087000-164089800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:164087600-164089800	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:164087600-164090200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:164087800-164089800	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:164087800-164089800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr6:164088000-164089600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:164088000-164089600	Enhancers	Brain Hippocampus Middle	brain
13	chr6:164088200-164089600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:164088200-164089600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:164088200-164089600	Enhancers	Primary T cells from cord blood	blood
16	chr6:164088200-164089800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:164088400-164093000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:164088600-164089600	Enhancers	K562	blood
19	chr6:164088600-164089800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:164088600-164089800	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr6:164089000-164089600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:164089000-164089600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr6:164089000-164089800	Flanking Active TSS	GM12878-XiMat	blood
24	chr6:164089000-164090800	Weak transcription	Brain Angular Gyrus	brain
25	chr6:164089200-164089800	Enhancers	Fetal Kidney	kidney
26	chr6:164089400-164089800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:164089400-164090200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr6:164089400-164090800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:164089400-164091400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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