Variant report

Variant	rs2060876
Chromosome Location	chr17:46322966-46322967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46321872..46325036-chr17:46699113..46702600,4	K562	blood:
2	chr17:46304803..46307483-chr17:46322659..46325078,2	K562	blood:
3	chr17:46322050..46323766-chr17:46722866..46724974,2	K562	blood:
4	chr17:46320871..46323469-chr17:46343037..46345002,2	K562	blood:
5	chr17:46316932..46321831-chr17:46322420..46326261,9	K562	blood:
6	chr17:46320855..46323440-chr17:46697694..46700613,3	K562	blood:

Variant related genes	Relation type
ENSG00000272763	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	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1010228	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs10445339	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10445377	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10853098	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11079806	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079808	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079814	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11651097	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11870056	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11872095	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12150533	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12452956	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12603115	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs12936731	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs12939334	0.82[ASN][1000 genomes]
rs12941830	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12946208	0.82[ASN][1000 genomes]
rs12947089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12948810	0.83[EUR][1000 genomes]
rs12952670	0.81[EUR][1000 genomes]
rs1316657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1377201	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1452667	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]
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];0.81[ASN][1000 genomes]
rs16954324	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs17620033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17681336	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1860862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1860863	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979897	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2021752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2021811	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2041572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051821	0.85[CHB][hapmap];0.81[JPT][hapmap]
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];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2109983	0.81[JPT][hapmap]
rs2109984	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2123341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[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];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2305433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2325804	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2924257	0.91[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2938483	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34949267	0.83[EUR][1000 genomes];0.86[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];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805363	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3805370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805371	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3897789	0.82[ASN][1000 genomes]
rs3897986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3944039	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4793779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4794447	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4794451	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4794505	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794517	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794525	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55982346	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62066447	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504025	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6504108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs66683298	0.82[AFR][1000 genomes]
rs67345313	0.82[ASN][1000 genomes]
rs6847	0.81[JPT][hapmap]
rs7210149	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7212202	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7213876	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7217496	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7219967	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7220768	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7220922	0.85[EUR][1000 genomes];0.86[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];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7224014	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7225435	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7225550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7225865	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7501770	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs758999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8065670	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8066391	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs8069064	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8069263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8075270	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077860	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs875065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs882380	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs954226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs978263	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9889470	0.82[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
rs2060876	SNX11	cis	Lymphoblastoid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46306600-46335400	Weak transcription	Thymus	Thymus
2	chr17:46315800-46323000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr17:46316400-46324600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:46317200-46324000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr17:46317800-46323000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:46319000-46324800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:46319600-46372000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:46319800-46323200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:46319800-46323600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr17:46319800-46324000	Weak transcription	Placenta	Placenta
11	chr17:46321000-46324800	Enhancers	NHEK	skin
12	chr17:46321400-46324200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:46321400-46325000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr17:46321800-46323000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr17:46321800-46325400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr17:46322000-46323800	Weak transcription	NH-A	brain
17	chr17:46322000-46324400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr17:46322000-46326000	Weak transcription	Fetal Thymus	thymus
19	chr17:46322400-46323200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr17:46322400-46323600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr17:46322400-46323600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr17:46322400-46323600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr17:46322400-46323800	Weak transcription	Primary T cells from cord blood	blood
24	chr17:46322400-46324000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:46322400-46328200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:46322400-46328200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr17:46322600-46323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:46322600-46323400	Enhancers	A549	lung
29	chr17:46322600-46323600	Weak transcription	GM12878-XiMat	blood
30	chr17:46322600-46323600	Weak transcription	HMEC	breast
31	chr17:46322600-46323600	Weak transcription	HSMM	muscle
32	chr17:46322600-46324000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr17:46322600-46324000	Weak transcription	NHDF-Ad	bronchial
34	chr17:46322600-46324600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr17:46322600-46325000	Enhancers	HUVEC	blood vessel
36	chr17:46322600-46328000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:46322600-46328200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr17:46322600-46328200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr17:46322600-46329400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr17:46322600-46341800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr17:46322600-46342200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr17:46322800-46323000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr17:46322800-46323200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr17:46322800-46323800	Weak transcription	Fetal Intestine Large	intestine
45	chr17:46322800-46324200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:46322800-46324400	Enhancers	K562	blood
47	chr17:46322800-46356200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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