Variant report

Variant	rs10089253
Chromosome Location	chr8:87446382-87446383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:87443232..87446931-chr8:87452708..87455402,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123124	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10086188	0.84[ASN][1000 genomes]
rs10089169	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10089317	0.89[EUR][1000 genomes]
rs10090898	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10090963	0.84[ASN][1000 genomes]
rs10092168	0.93[ASN][1000 genomes]
rs10093867	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10094332	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10095589	0.84[ASN][1000 genomes]
rs10097546	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10097866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10098365	0.84[ASN][1000 genomes]
rs10100182	0.93[ASN][1000 genomes]
rs10100247	0.84[ASN][1000 genomes]
rs10100254	0.90[ASN][1000 genomes]
rs10100368	0.93[ASN][1000 genomes]
rs10100698	0.89[EUR][1000 genomes]
rs10106390	0.84[ASN][1000 genomes]
rs10107117	0.84[ASN][1000 genomes]
rs10107571	0.84[ASN][1000 genomes]
rs10108586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10109677	0.87[EUR][1000 genomes]
rs10110096	0.93[ASN][1000 genomes]
rs10110323	0.94[EUR][1000 genomes]
rs10481195	1.00[ASN][1000 genomes]
rs10504823	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10956820	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10956821	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10956822	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10956871	0.84[ASN][1000 genomes]
rs11774253	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11774499	0.84[ASN][1000 genomes]
rs11776698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781993	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11783382	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11984519	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11986423	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11994508	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11997927	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11998558	1.00[ASN][1000 genomes]
rs12155979	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12155981	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12156004	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12216783	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12335013	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13265266	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16915375	0.84[ASN][1000 genomes]
rs16915389	0.84[ASN][1000 genomes]
rs17681534	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17681826	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28384362	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28397606	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28416254	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28433311	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28438974	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28504479	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28514445	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28540009	0.84[ASN][1000 genomes]
rs28613262	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28680173	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28687116	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28715255	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2917553	0.85[EUR][1000 genomes]
rs2953518	0.85[EUR][1000 genomes]
rs2953519	0.85[EUR][1000 genomes]
rs2953521	0.82[EUR][1000 genomes]
rs2976170	0.85[EUR][1000 genomes]
rs2976173	0.85[EUR][1000 genomes]
rs2976174	0.84[EUR][1000 genomes]
rs2976175	0.85[EUR][1000 genomes]
rs2976176	0.85[EUR][1000 genomes]
rs2976194	0.89[EUR][1000 genomes]
rs3087641	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4440616	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55671538	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55871514	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57638937	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58837061	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471295	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6471317	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6651177	0.84[ASN][1000 genomes]
rs6651268	0.84[ASN][1000 genomes]
rs67332431	0.93[ASN][1000 genomes]
rs6980476	0.84[ASN][1000 genomes]
rs6992624	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6993497	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6993612	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7015772	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7018083	0.88[ASN][1000 genomes]
rs72690416	0.93[ASN][1000 genomes]
rs72690443	0.84[ASN][1000 genomes]
rs72690445	0.84[ASN][1000 genomes]
rs72690447	0.84[ASN][1000 genomes]
rs72690455	0.84[ASN][1000 genomes]
rs72690457	0.84[ASN][1000 genomes]
rs72690474	0.84[ASN][1000 genomes]
rs73688817	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73688823	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73688824	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73688827	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73688856	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73688857	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73688858	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73688859	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73688862	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7818436	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7823951	0.81[ASN][1000 genomes]
rs7824873	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7833201	0.81[ASN][1000 genomes]
rs7837581	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7837618	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7839096	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7843272	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7843399	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7844014	0.84[ASN][1000 genomes]
rs9297913	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9650128	0.84[ASN][1000 genomes]
rs9650129	0.84[ASN][1000 genomes]
rs9656823	0.84[EUR][1000 genomes]
rs9656824	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10089253	FAM82B///LOC642197	Cis_1M	lymphoblastoid	RTeQTL
rs10089253	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87426000-87446400	Weak transcription	K562	blood
2	chr8:87427400-87452600	Weak transcription	HSMMtube	muscle
3	chr8:87427600-87485600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr8:87428600-87460800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr8:87429400-87453600	Weak transcription	Stomach Mucosa	stomach
6	chr8:87432600-87451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:87436400-87451800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr8:87436800-87451600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr8:87436800-87483200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr8:87437200-87450400	Strong transcription	Dnd41	blood
11	chr8:87437400-87451400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr8:87437400-87451600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr8:87437400-87451800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:87437400-87451800	Strong transcription	Fetal Lung	lung
15	chr8:87437400-87452200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr8:87437400-87452600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr8:87437400-87453000	Strong transcription	Liver	Liver
18	chr8:87437400-87456400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr8:87437400-87457800	Strong transcription	Fetal Thymus	thymus
20	chr8:87437400-87458000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:87437400-87458000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr8:87437400-87458200	Strong transcription	Placenta	Placenta
23	chr8:87437400-87482800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr8:87437600-87448800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr8:87437600-87451600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:87437600-87452000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr8:87437800-87489600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr8:87438000-87451600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr8:87438000-87451800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr8:87438000-87457800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr8:87438600-87449400	Strong transcription	Left Ventricle	heart
32	chr8:87438600-87452600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:87439600-87454200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr8:87440600-87451800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr8:87440800-87450800	Strong transcription	Fetal Muscle Leg	muscle
36	chr8:87440800-87451400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:87441800-87507600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr8:87442200-87454800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr8:87442800-87449200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr8:87442800-87475600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr8:87443000-87478800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr8:87443400-87449200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr8:87443400-87451600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:87443400-87452000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr8:87443400-87452200	Strong transcription	Adipose Nuclei	Adipose
46	chr8:87443400-87452800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr8:87443400-87455000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:87443400-87457800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr8:87443600-87448400	Strong transcription	Thymus	Thymus
50	chr8:87443600-87448400	Strong transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links