Variant report

Variant	rs1452667
Chromosome Location	chr17:46302415-46302416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46297342..46300258-chr17:46302052..46303891,2	K562	blood:
2	chr17:46300743..46302488-chr17:46304073..46305915,2	K562	blood:
3	chr17:46301515..46304041-chr17:46368069..46369747,2	K562	blood:
4	chr17:46300434..46303354-chr17:46310850..46313600,3	K562	blood:
5	chr17:46301003..46302784-chr17:46314559..46316930,2	K562	blood:
6	chr17:46300980..46304864-chr17:46703417..46705646,3	K562	blood:

Variant related genes	Relation type
ENSG00000170689	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1002330	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1010228	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10445339	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10445377	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853098	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079806	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079808	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079814	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11651097	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11870056	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11872095	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12150533	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12452956	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12603115	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs12936731	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs12939334	0.84[ASN][1000 genomes]
rs12941830	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12946208	0.84[ASN][1000 genomes]
rs12947089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12948810	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12952670	0.81[EUR][1000 genomes]
rs1316657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1377201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452663	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1452665	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1452666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468270	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs16951519	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs16953941	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs16954268	0.85[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs16954324	0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs17620033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17681336	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1860862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1860863	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1979897	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2021752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2021811	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2041572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072441	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs208005	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208008	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208009	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208015	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2109982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2109983	0.80[JPT][hapmap]
rs2109984	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2123341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[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];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2325804	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2924257	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2938483	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34949267	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3744346	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3792692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3805363	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3805370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3805371	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3897789	0.84[ASN][1000 genomes]
rs3897986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3944039	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4793779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4794447	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4794451	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4794505	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794517	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4794525	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55982346	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62066447	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6504025	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6504108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs67345313	0.84[ASN][1000 genomes]
rs6847	0.81[JPT][hapmap]
rs7210149	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7212202	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7213876	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7217496	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7219967	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7220619	0.80[ASN][1000 genomes]
rs7220768	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7220922	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7222136	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7223867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7224014	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7225435	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7225550	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]
rs7225865	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7501770	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs758999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8065670	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8066391	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs8069064	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8069263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[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];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8075270	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8077860	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs875065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs882380	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs954226	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978263	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9889470	0.84[ASN][1000 genomes]
rs9899275	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9899461	0.85[CHB][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1452667	SNX11	cis	Lymphoblastoid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46266800-46318200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr17:46273200-46302800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:46273200-46314000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:46283600-46314000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr17:46288400-46307000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr17:46294000-46318000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46295000-46304400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:46295200-46303000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:46295800-46303200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr17:46295800-46314200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr17:46297400-46302800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr17:46297600-46314400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:46297800-46302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:46298000-46306000	Weak transcription	K562	blood
15	chr17:46299400-46302600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:46301000-46302800	Enhancers	HUVEC	blood vessel
17	chr17:46301200-46314000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr17:46301600-46302600	Enhancers	GM12878-XiMat	blood
19	chr17:46302000-46302600	Enhancers	Primary T cells from cord blood	blood
20	chr17:46302000-46304000	Weak transcription	A549	lung
21	chr17:46302200-46302600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr17:46302200-46303200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr17:46302200-46303800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr17:46302200-46305800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr17:46302400-46302800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr17:46302400-46303400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr17:46302400-46303600	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links