Variant report

Variant	rs1568954
Chromosome Location	chr15:52853428-52853429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52585466..52588318-chr15:52852400..52853914,2	MCF-7	breast:
2	chr15:52844956..52846516-chr15:52850734..52853652,2	MCF-7	breast:
3	chr15:52721087..52722609-chr15:52853410..52856403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12232368	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592429	0.80[GIH][hapmap];1.00[MEX][hapmap]
rs12899847	0.88[MEX][hapmap]
rs12915892	1.00[ASW][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs1724593	0.82[MEX][hapmap]
rs2414159	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34197242	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35014728	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57187323	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493566	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7181784	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1568954	SECISBP2L	cis	parietal	SCAN
rs1568954	MYO5A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
2	chr15:52838800-52859800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:52838800-52860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:52839000-52858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:52839000-52859600	Weak transcription	Aorta	Aorta
6	chr15:52839200-52859200	Weak transcription	Colonic Mucosa	Colon
7	chr15:52841000-52857400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:52842400-52858400	Weak transcription	Pancreas	Pancrea
9	chr15:52844400-52855200	Weak transcription	Fetal Lung	lung
10	chr15:52844400-52859200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:52844600-52856400	Weak transcription	Ovary	ovary
12	chr15:52844600-52859000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:52844800-52860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:52845200-52854200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:52845200-52857200	Weak transcription	Fetal Stomach	stomach
16	chr15:52846200-52855800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:52846200-52857200	Weak transcription	Thymus	Thymus
18	chr15:52846200-52859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:52846200-52860000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:52847000-52859400	Weak transcription	Fetal Intestine Large	intestine
21	chr15:52849400-52857200	Weak transcription	Fetal Thymus	thymus
22	chr15:52849400-52857400	Weak transcription	Primary T cells from cord blood	blood
23	chr15:52849400-52857400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:52849400-52859000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:52849400-52860000	Weak transcription	Placenta	Placenta
26	chr15:52849600-52857400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:52849800-52855800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:52849800-52857200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:52850000-52859200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:52850200-52853600	Genic enhancers	A549	lung
31	chr15:52850200-52858200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:52850200-52859200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:52850400-52854200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:52850800-52857200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr15:52850800-52857200	Weak transcription	Fetal Brain Male	brain
36	chr15:52850800-52859000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:52850800-52859000	Weak transcription	HSMMtube	muscle
38	chr15:52851000-52853600	Enhancers	Brain Hippocampus Middle	brain
39	chr15:52851000-52853600	Strong transcription	Hela-S3	cervix
40	chr15:52851200-52853600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr15:52851200-52856400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:52851400-52853600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:52851400-52853800	Enhancers	Fetal Heart	heart
44	chr15:52851600-52859200	Weak transcription	Fetal Kidney	kidney
45	chr15:52851600-52859200	Weak transcription	HSMM	muscle
46	chr15:52851800-52855800	Weak transcription	Right Atrium	heart
47	chr15:52851800-52856000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:52852000-52855800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:52852000-52856400	Weak transcription	Esophagus	oesophagus
50	chr15:52852000-52856400	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links