Variant report

Variant	rs8071879
Chromosome Location	chr17:46217457-46217458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1010228	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs10514944	0.89[TSI][hapmap]
rs11079806	1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs11079808	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs11651097	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs12936731	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12946679	0.82[YRI][hapmap]
rs12947089	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs12948214	1.00[YRI][hapmap]
rs12950437	0.82[YRI][hapmap]
rs1316657	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1452663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1452665	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1452666	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1452667	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1468270	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs16951519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16952687	1.00[YRI][hapmap]
rs16953941	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];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16954268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16954324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17616799	0.88[GIH][hapmap]
rs17620033	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs17694092	0.95[TSI][hapmap]
rs17694404	0.95[TSI][hapmap]
rs1860862	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1979897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs2021752	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2023885	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2041572	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2051821	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs2060876	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208005	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs208008	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs208009	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];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs208015	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2109982	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2109983	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2109984	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs2123341	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2229369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2240119	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2240120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2240121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2240122	1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs2278868	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2285860	0.91[CEU][hapmap];0.94[GIH][hapmap]
rs2305433	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2325804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2525105	0.94[GIH][hapmap]
rs3744346	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3792692	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs3792694	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs3805370	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs3897986	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4793779	0.83[CHB][hapmap]
rs4794447	0.83[CHB][hapmap]
rs4794451	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs6504025	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6504108	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs6847	0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs7212202	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7217496	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs7220520	0.95[CHD][hapmap];0.80[JPT][hapmap]
rs7220768	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7222136	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7223867	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs7224014	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7224461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7225550	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs757353	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs758999	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs8065670	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs8066391	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs8069263	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8071199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8072282	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8077860	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs875065	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs978263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs9899275	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs9899461	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs8071879	KRT37	cis	cerebellum	SCAN
rs8071879	CDK5RAP3	cis	cerebellum	SCAN
rs8071879	CDK5RAP3	cis	parietal	SCAN
rs8071879	CBX1	cis	cerebellum	SCAN
rs8071879	CBX1	Cis_1M	lymphoblastoid	RTeQTL
rs8071879	TUBG1	cis	parietal	SCAN
rs8071879	HOXB7	cis	cerebellum	SCAN
rs8071879	SNX11	cis	lymphoblastoid	seeQTL
rs8071879	HSPB9	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46191200-46220800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:46197800-46221000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr17:46201400-46217600	Weak transcription	Fetal Thymus	thymus
5	chr17:46204000-46220000	Weak transcription	GM12878-XiMat	blood
6	chr17:46204200-46225200	Weak transcription	Liver	Liver
7	chr17:46204400-46221000	Weak transcription	Thymus	Thymus
8	chr17:46206400-46220800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:46210000-46224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:46211200-46231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr17:46212400-46234800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr17:46213400-46220800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:46215400-46225400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:46215600-46219000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr17:46216600-46218000	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr17:46216600-46219000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr17:46216600-46235600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr17:46216800-46219600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr17:46217000-46217600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:46217000-46217600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:46217000-46217800	Enhancers	HUVEC	blood vessel
23	chr17:46217000-46218000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr17:46217000-46218000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:46217000-46218000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr17:46217000-46218200	Enhancers	Primary hematopoietic stem cells	blood
27	chr17:46217000-46218200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr17:46217000-46219800	Strong transcription	Primary T cells from cord blood	blood
29	chr17:46217400-46217600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr17:46217400-46218000	Enhancers	Primary B cells from cord blood	blood
31	chr17:46217400-46218000	Enhancers	Primary B cells from peripheral blood	blood
32	chr17:46217400-46218200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood

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