Variant report

Variant	rs17430251
Chromosome Location	chr4:106115708-106115709
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	chr4:106064689..106068216-chr4:106113083..106116896,4	MCF-7	breast:
2	chr4:106114330..106115965-chr4:106120710..106122443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11728350	0.94[GIH][hapmap];0.87[EUR][1000 genomes]
rs1498125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1498126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs17035310	0.88[GIH][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs17320054	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17508261	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34402524	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464576	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs56185013	0.91[ASN][1000 genomes]
rs6825684	0.94[GIH][hapmap];0.90[EUR][1000 genomes]
rs72665951	0.82[ASN][1000 genomes]
rs763480	0.83[GIH][hapmap];0.87[EUR][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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17430251	BDH2	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
2	chr4:106101000-106146600	Weak transcription	Spleen	Spleen
3	chr4:106102800-106127400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:106104800-106117400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:106105200-106117800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:106106000-106135000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:106106200-106118600	Weak transcription	Thymus	Thymus
8	chr4:106106200-106155000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:106106600-106125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:106108000-106123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:106110600-106118600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:106111000-106118800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:106111200-106117200	Genic enhancers	Primary monocytes fromperipheralblood	blood
14	chr4:106111800-106127400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:106112200-106127200	Weak transcription	Primary T cells from cord blood	blood
16	chr4:106112400-106116600	Enhancers	Osteobl	bone
17	chr4:106112400-106127000	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:106112600-106117000	Genic enhancers	Monocytes-CD14+_RO01746	blood
19	chr4:106112800-106116400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:106112800-106116400	Enhancers	NHDF-Ad	bronchial
21	chr4:106112800-106116400	Enhancers	NHEK	skin
22	chr4:106112800-106127400	Weak transcription	Placenta	Placenta
23	chr4:106113000-106118000	Weak transcription	Ovary	ovary
24	chr4:106113000-106120400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:106113000-106126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:106113000-106127200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:106113000-106154800	Weak transcription	Fetal Thymus	thymus
28	chr4:106113200-106116200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:106113200-106136000	Weak transcription	Brain Anterior Caudate	brain
30	chr4:106113200-106136000	Weak transcription	Brain Substantia Nigra	brain
31	chr4:106113200-106136800	Weak transcription	Fetal Kidney	kidney
32	chr4:106113200-106146600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:106113400-106117000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr4:106113400-106120600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr4:106113400-106123800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:106113600-106116000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:106113600-106117200	Weak transcription	Brain Hippocampus Middle	brain
38	chr4:106113600-106117400	Weak transcription	Fetal Intestine Small	intestine
39	chr4:106113600-106117800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:106113600-106136000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:106113600-106173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:106114000-106117800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:106114000-106118000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:106114000-106118600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:106114200-106117800	Weak transcription	A549	lung
47	chr4:106114200-106118800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:106114400-106116000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr4:106114400-106116000	Weak transcription	HSMMtube	muscle
50	chr4:106114400-106117200	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links