Variant report

Variant	rs3792693
Chromosome Location	chr17:46260366-46260367
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	chr17:46258902..46261655-chr17:46700087..46701863,2	K562	blood:
2	chr17:46252245..46255136-chr17:46259026..46261295,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10853093	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs11079815	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11079817	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11651669	0.87[CHD][hapmap]
rs11655781	0.87[CHD][hapmap]
rs12452103	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12952089	0.82[EUR][1000 genomes]
rs1349676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1377201	1.00[CHB][hapmap]
rs1452661	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1910574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs208006	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs208007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs208013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs208017	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];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs208018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2123342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2325886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28439030	0.85[EUR][1000 genomes]
rs28551638	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2924253	1.00[CHB][hapmap]
rs2924255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2924256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2924258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2938471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2938480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2938482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2957932	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs2957933	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs3792695	0.83[EUR][1000 genomes]
rs4794426	0.83[EUR][1000 genomes]
rs4794427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs4794467	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4794488	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs5016303	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs595874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6504100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207270	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7208796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7213530	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7216766	0.84[EUR][1000 genomes]
rs7218167	0.87[CHD][hapmap]
rs7220940	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7225140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8066529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8071262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8077814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8081199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8182234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9303544	0.82[CHD][hapmap]
rs979746	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs9893405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9899753	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3792693	MLX	cis	cerebellum	SCAN
rs3792693	AARSD1	cis	parietal	SCAN
rs3792693	HOXB2	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46251200-46267200	Strong transcription	Primary T cells from cord blood	blood
2	chr17:46251200-46277400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr17:46251800-46267400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr17:46252000-46271400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr17:46252600-46271000	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr17:46253200-46270800	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr17:46253400-46260800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr17:46253600-46267000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
9	chr17:46253800-46266800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr17:46254000-46271000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:46254400-46260400	Strong transcription	Fetal Thymus	thymus
12	chr17:46254400-46266800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr17:46255000-46270800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:46255200-46270800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:46256800-46262000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:46256800-46268400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:46257000-46266200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr17:46257400-46260400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:46257400-46262400	Weak transcription	HSMMtube	muscle
20	chr17:46257600-46262000	Weak transcription	Thymus	Thymus
21	chr17:46259400-46261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:46259600-46261600	Weak transcription	GM12878-XiMat	blood
23	chr17:46260000-46261400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:46260200-46260400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr17:46260200-46260600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr17:46260200-46260600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr17:46260200-46260600	Enhancers	HSMM	muscle
28	chr17:46260200-46261600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:46260200-46261600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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