Variant report

Variant	rs17026610
Chromosome Location	chr2:85975594-85975595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr2:85975108-85975751	GM12878	blood:	n/a	n/a
2	SPI1	chr2:85974790-85975833	GM12878	blood:	n/a	n/a
3	STAT5A	chr2:85975124-85975624	GM12878	blood:	n/a	n/a
4	EBF1	chr2:85975199-85975633	GM12878	blood:	n/a	chr2:85975485-85975496
5	RUNX3	chr2:85975121-85975632	GM12878	blood:	n/a	n/a
6	SPI1	chr2:85975035-85975622	GM12891	blood:	n/a	n/a
7	BCLAF1	chr2:85975174-85975610	GM12878	blood:	n/a	n/a
8	RUNX3	chr2:85975092-85975622	GM12878	blood:	n/a	n/a
9	EBF1	chr2:85975200-85975652	GM12878	blood:	n/a	chr2:85975485-85975496
10	EP300	chr2:85975106-85975595	GM12878	blood:	n/a	n/a
11	IRF4	chr2:85975057-85975620	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85959891..85961430-chr2:85975278..85976868,2	MCF-7	breast:
2	chr2:85968047..85970017-chr2:85974638..85977440,3	MCF-7	breast:
3	chr2:85974895..85977251-chr2:85979669..85982640,2	MCF-7	breast:

Variant related genes	Relation type
ATOH8	TF binding region
ENSG00000168874	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17026608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366814	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2366815	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55678683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085927	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59731035	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743301	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6750921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1012593	chr2:85966323-85997189	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85971600-85977800	Weak transcription	Pancreas	Pancrea
2	chr2:85972200-85976200	Weak transcription	Gastric	stomach
3	chr2:85972400-85975800	Weak transcription	Hela-S3	cervix
4	chr2:85972400-85976200	Weak transcription	Stomach Mucosa	stomach
5	chr2:85972400-85976800	Enhancers	Primary B cells from cord blood	blood
6	chr2:85972400-85978200	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:85972800-85975600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:85972800-85975800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:85972800-85976000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:85972800-85977800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:85973000-85977800	Weak transcription	Brain Germinal Matrix	brain
12	chr2:85973000-85979000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:85973200-85976000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:85973400-85980200	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr2:85973600-85975800	Weak transcription	Aorta	Aorta
16	chr2:85973600-85976000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:85973800-85975600	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:85973800-85975800	Weak transcription	HSMM	muscle
19	chr2:85973800-85976000	Weak transcription	Brain Angular Gyrus	brain
20	chr2:85973800-85976000	Weak transcription	Brain Anterior Caudate	brain
21	chr2:85973800-85976000	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:85973800-85976000	Weak transcription	Ovary	ovary
23	chr2:85973800-85976000	Weak transcription	Spleen	Spleen
24	chr2:85973800-85976600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:85973800-85977800	Weak transcription	Esophagus	oesophagus
26	chr2:85974000-85975800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:85974000-85975800	Weak transcription	NHDF-Ad	bronchial
28	chr2:85974000-85976000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:85974000-85976200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:85974200-85975600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:85974200-85976000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:85974400-85975800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:85974600-85976400	ZNF genes & repeats	GM12878-XiMat	blood
34	chr2:85974600-85976800	Enhancers	Right Atrium	heart
35	chr2:85974600-85977600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr2:85974800-85975600	Weak transcription	Brain Substantia Nigra	brain
37	chr2:85974800-85975800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:85974800-85976000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:85974800-85980400	Enhancers	Fetal Heart	heart
40	chr2:85975000-85976200	Enhancers	HSMMtube	muscle
41	chr2:85975000-85978000	Enhancers	Adipose Nuclei	Adipose
42	chr2:85975200-85975600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr2:85975200-85976000	Weak transcription	Osteobl	bone
44	chr2:85975200-85976200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr2:85975200-85976800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:85975200-85977000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr2:85975200-85977200	Enhancers	Psoas Muscle	Psoas
48	chr2:85975200-85977200	Enhancers	Right Ventricle	heart
49	chr2:85975200-85979400	Enhancers	Fetal Lung	lung
50	chr2:85975400-85975600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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