Variant report

Variant	rs7225550
Chromosome Location	chr17:46225243-46225244
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	chr17:46224894..46227721-chr17:46229708..46233601,3	MCF-7	breast:
2	chr17:46224844..46227376-chr17:46230087..46232594,2	MCF-7	breast:

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1002330	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1010228	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1010230	0.80[ASN][1000 genomes]
rs10445339	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10445377	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853098	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079806	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079808	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079809	0.80[ASN][1000 genomes]
rs11079814	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11651097	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11870056	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11872095	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150533	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12452956	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12603115	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12603380	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12936369	0.82[ASN][1000 genomes]
rs12936731	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs12941830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948810	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1316657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1377201	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1452662	0.80[ASN][1000 genomes]
rs1452663	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1452665	0.86[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1452666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1452667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468270	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs16951519	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs16953927	0.80[ASN][1000 genomes]
rs16953941	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs16954268	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs16954324	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs17620033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17681336	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1860863	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1860866	0.80[ASN][1000 genomes]
rs1979897	0.86[CHB][hapmap]
rs2021752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021811	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051821	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2060876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2072441	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs208005	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs208008	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs208009	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs208011	0.82[ASN][1000 genomes]
rs208012	0.82[ASN][1000 genomes]
rs208015	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208019	0.84[ASN][1000 genomes]
rs2109982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2109983	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2109984	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2123341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2229369	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2240120	0.85[CHB][hapmap]
rs2240121	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2240122	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2278868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2325784	0.83[ASN][1000 genomes]
rs2325804	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2325885	0.80[ASN][1000 genomes]
rs2924257	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs2938483	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34949267	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34980108	0.80[ASN][1000 genomes]
rs36071506	0.80[ASN][1000 genomes]
rs3744346	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3792692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805363	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805371	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815472	0.84[ASN][1000 genomes]
rs3897986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3944039	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794447	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4794451	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4794505	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794517	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794525	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55696440	0.82[ASN][1000 genomes]
rs55982346	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62066407	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62066447	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504025	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6504108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs66683298	0.82[EUR][1000 genomes]
rs67446770	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6847	0.81[JPT][hapmap]
rs71356521	0.82[ASN][1000 genomes]
rs7209730	0.80[ASN][1000 genomes]
rs7210149	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7212202	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7213876	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7217496	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7219967	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7220619	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7220768	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7220922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222136	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7223867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224014	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7224461	0.80[ASN][1000 genomes]
rs7225435	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7225865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741058	0.80[ASN][1000 genomes]
rs7501770	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs758999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8065670	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8066391	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs8069064	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8069263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8071199	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8071879	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8072282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8075270	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8077860	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8079616	0.84[ASN][1000 genomes]
rs875065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs882380	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954226	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978263	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9807087	0.80[ASN][1000 genomes]
rs9899275	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9899461	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9903692	0.82[ASN][1000 genomes]
rs9909933	0.80[ASN][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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7225550	SNX11	cis	Lymphoblastoid	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:46211200-46231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:46212400-46234800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr17:46215400-46225400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr17:46216600-46235600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr17:46220600-46225600	Strong transcription	Primary T cells from cord blood	blood
8	chr17:46220800-46227200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr17:46220800-46228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:46221200-46228000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr17:46221400-46230800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:46221600-46225400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:46221600-46225400	Weak transcription	Thymus	Thymus
15	chr17:46221600-46225600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:46221600-46226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:46221600-46238400	Weak transcription	Fetal Thymus	thymus
18	chr17:46222800-46234600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:46223200-46226600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:46223200-46228400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:46223400-46226400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr17:46223400-46226600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:46224200-46225400	Strong transcription	GM12878-XiMat	blood
24	chr17:46224200-46226200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
25	chr17:46224400-46227200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:46224800-46225400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:46224800-46226600	Bivalent Enhancer	Fetal Brain Male	brain
28	chr17:46225000-46226800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:46225200-46225400	Bivalent Enhancer	Colon Smooth Muscle	Colon
30	chr17:46225200-46225800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr17:46225200-46226000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr17:46225200-46226000	Strong transcription	Liver	Liver
33	chr17:46225200-46226600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links