Variant report

Variant	rs2297139
Chromosome Location	chr1:86038234-86038235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86036311..86039130-chr1:86039970..86042823,4	MCF-7	breast:
2	chr1:86011310..86014222-chr1:86037921..86041658,3	MCF-7	breast:
3	chr1:86034192..86035799-chr1:86036306..86038503,2	K562	blood:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12566306	1.00[ASW][hapmap]
rs12566318	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs17127878	0.81[CHD][hapmap];0.91[MEX][hapmap]
rs17128092	1.00[ASW][hapmap]
rs17390740	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2297138	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658584	0.94[CEU][hapmap];0.85[TSI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297139	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86032800-86042000	Weak transcription	Left Ventricle	heart
2	chr1:86034000-86041800	Enhancers	HMEC	breast
3	chr1:86034600-86041400	Weak transcription	Lung	lung
4	chr1:86034800-86041200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:86035200-86038400	Weak transcription	Esophagus	oesophagus
6	chr1:86035200-86041400	Enhancers	HUVEC	blood vessel
7	chr1:86035400-86041000	Genic enhancers	Muscle Satellite Cultured Cells	--
8	chr1:86035400-86041400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:86035400-86041800	Weak transcription	Right Ventricle	heart
10	chr1:86035600-86041800	Weak transcription	Ovary	ovary
11	chr1:86035600-86042000	Weak transcription	Placenta	Placenta
12	chr1:86036200-86040000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:86036200-86041800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:86036200-86042200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:86036400-86041000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:86036400-86041800	Weak transcription	A549	lung
17	chr1:86036600-86041000	Weak transcription	Fetal Heart	heart
18	chr1:86036600-86041200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:86036800-86038600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:86036800-86041800	Enhancers	Hela-S3	cervix
21	chr1:86037000-86038600	Enhancers	Fetal Stomach	stomach
22	chr1:86037000-86040600	Genic enhancers	NHLF	lung
23	chr1:86037000-86040800	Genic enhancers	HSMM	muscle
24	chr1:86037200-86038400	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:86037200-86038400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:86037400-86039000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:86037400-86039200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:86037400-86040200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:86037400-86041800	Weak transcription	Fetal Kidney	kidney
30	chr1:86037600-86038400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:86037600-86038600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:86037600-86038600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:86037600-86038600	Genic enhancers	HSMMtube	muscle
34	chr1:86037800-86038600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:86037800-86039400	Genic enhancers	Osteobl	bone
36	chr1:86037800-86041200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:86037800-86041200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:86037800-86041200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:86037800-86042000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:86038000-86038400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:86038000-86038600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:86038000-86038600	Flanking Active TSS	NHEK	skin
43	chr1:86038000-86039800	Weak transcription	HepG2	liver
44	chr1:86038000-86040000	Genic enhancers	NH-A	brain
45	chr1:86038000-86040400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:86038000-86041800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:86038200-86038600	Genic enhancers	Aorta	Aorta
48	chr1:86038200-86040200	Enhancers	NHDF-Ad	bronchial
49	chr1:86038200-86040600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links