Variant report

Variant	rs2890827
Chromosome Location	chr8:95538468-95538469
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	chr8:95536103..95541001-chr8:95541149..95546680,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254315	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11784188	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11786245	0.87[ASN][1000 genomes]
rs11992717	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17716313	0.83[CEU][hapmap]
rs1866844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs1978556	0.85[ASN][1000 genomes]
rs2304765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3096604	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3098705	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3098711	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs3098714	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098722	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099405	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3099414	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3099422	0.85[ASN][1000 genomes]
rs3099425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3102852	0.86[ASN][1000 genomes]
rs3102854	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3102856	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102857	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3102865	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133600	0.87[ASN][1000 genomes]
rs3133636	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3133639	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3133646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv611750	chr8:95519205-95574634	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2890827	TSPYL5	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95493000-95549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:95495600-95541000	Weak transcription	Esophagus	oesophagus
3	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:95498400-95554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:95499400-95552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:95501200-95541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:95516800-95554600	Strong transcription	Fetal Thymus	thymus
8	chr8:95517600-95538600	Weak transcription	Fetal Brain Male	brain
9	chr8:95517600-95540200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:95520400-95555200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr8:95520600-95552400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr8:95523800-95539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr8:95524000-95540400	Weak transcription	Colonic Mucosa	Colon
14	chr8:95527600-95548600	Strong transcription	Fetal Muscle Leg	muscle
15	chr8:95528000-95542400	Weak transcription	Pancreas	Pancrea
16	chr8:95528400-95540800	Weak transcription	Spleen	Spleen
17	chr8:95528400-95541200	Weak transcription	Right Ventricle	heart
18	chr8:95528400-95542400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:95531600-95538600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr8:95531600-95540200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr8:95531600-95540800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr8:95531800-95538600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr8:95532000-95538600	Weak transcription	NHDF-Ad	bronchial
24	chr8:95532800-95558800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr8:95534000-95543600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr8:95534200-95539800	Strong transcription	Primary T cells from cord blood	blood
27	chr8:95534200-95545000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr8:95535400-95556000	Weak transcription	Fetal Heart	heart
29	chr8:95535800-95540800	Weak transcription	Small Intestine	intestine
30	chr8:95535800-95549800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:95535800-95555600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr8:95536000-95539800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:95536000-95555600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:95536200-95541000	Weak transcription	Stomach Mucosa	stomach
35	chr8:95536200-95549200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr8:95536400-95552200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr8:95536600-95541400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr8:95536600-95542400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr8:95536600-95557000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr8:95536800-95539600	Strong transcription	HSMM	muscle
41	chr8:95536800-95543200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr8:95536800-95543400	Strong transcription	Brain Germinal Matrix	brain
43	chr8:95536800-95546600	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr8:95536800-95549800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr8:95536800-95550600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr8:95536800-95551400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr8:95536800-95552400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr8:95536800-95556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:95537000-95539200	Strong transcription	NHLF	lung
50	chr8:95537000-95539600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links