Variant report

Variant	rs17177041
Chromosome Location	chr14:71242458-71242459
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	chr14:71233318..71235646-chr14:71241902..71243405,2	MCF-7	breast:
2	chr14:71237788..71240582-chr14:71241825..71244076,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11625206	1.00[JPT][hapmap]
rs17176971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17177041	DNAL1	cis	cerebellum	SCAN
rs17177041	MAP3K9	cis	cerebellum	SCAN
rs17177041	PSEN1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71216600-71245800	Weak transcription	Brain Germinal Matrix	brain
2	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
3	chr14:71222200-71258200	Weak transcription	HepG2	liver
4	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
5	chr14:71223000-71258400	Weak transcription	Primary T cells from cord blood	blood
6	chr14:71223000-71266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:71224000-71258000	Weak transcription	Dnd41	blood
8	chr14:71227800-71245200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr14:71227800-71245600	Weak transcription	Lung	lung
10	chr14:71227800-71257800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr14:71228000-71245600	Weak transcription	Gastric	stomach
12	chr14:71228000-71258000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr14:71228000-71258000	Weak transcription	A549	lung
14	chr14:71228200-71251400	Weak transcription	Fetal Brain Female	brain
15	chr14:71228200-71258000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr14:71238600-71266600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr14:71238800-71244000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:71239000-71244000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr14:71239000-71247600	Weak transcription	Esophagus	oesophagus
20	chr14:71239000-71252400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr14:71239000-71258000	Weak transcription	Fetal Intestine Small	intestine
22	chr14:71239000-71269600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr14:71239200-71243800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:71239200-71244000	Weak transcription	NHEK	skin
25	chr14:71239200-71258200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:71239400-71258200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr14:71239800-71243600	Strong transcription	HMEC	breast
28	chr14:71239800-71258400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr14:71240000-71258000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr14:71240200-71257800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr14:71240600-71250400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:71240600-71255600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr14:71240600-71258000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:71240800-71250200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:71241000-71246000	Weak transcription	Liver	Liver
36	chr14:71242000-71242600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr14:71242000-71242600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr14:71242000-71243000	Enhancers	GM12878-XiMat	blood
39	chr14:71242400-71258200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr14:71242400-71266600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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