Variant report

Variant	rs2959080
Chromosome Location	chr11:4028447-4028448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10734400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10742194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10742207	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10767775	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835500	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030584	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11602757	0.90[GIH][hapmap];0.89[MKK][hapmap]
rs1465952	0.93[LWK][hapmap];0.96[MKK][hapmap]
rs2289570	0.90[GIH][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap]
rs2860454	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898950	0.90[GIH][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap]
rs2920137	0.90[GIH][hapmap]
rs2920142	0.90[GIH][hapmap]
rs2923946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2923958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2923959	0.91[AFR][1000 genomes]
rs2959058	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2959059	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4379839	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910595	0.90[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap]
rs6578430	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7114777	0.85[AFR][1000 genomes]
rs727152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928763	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7945918	0.93[LWK][hapmap];0.97[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2959080	DCHS1	cis	parietal	SCAN
rs2959080	ANO9	cis	parietal	SCAN
rs2959080	KRTAP5-4	cis	cerebellum	SCAN
rs2959080	RRM1	cis	parietal	SCAN
rs2959080	TRIM21	cis	cerebellum	SCAN
rs2959080	RRM1	cis	cerebellum	SCAN
rs2959080	IFITM5	cis	cerebellum	SCAN
rs2959080	C11orf21	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3989400-4031000	Weak transcription	Aorta	Aorta
2	chr11:4017400-4041400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:4017600-4043400	Weak transcription	Primary B cells from cord blood	blood
4	chr11:4020800-4037600	Weak transcription	Pancreas	Pancrea
5	chr11:4020800-4045000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:4021000-4032200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:4021000-4043600	Weak transcription	Thymus	Thymus
8	chr11:4021000-4044200	Weak transcription	Fetal Thymus	thymus
9	chr11:4021000-4044400	Weak transcription	Dnd41	blood
10	chr11:4027000-4028800	Enhancers	Primary T cells from cord blood	blood
11	chr11:4027000-4028800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:4027000-4029200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr11:4027000-4029200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr11:4027000-4029200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr11:4027000-4029600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr11:4027000-4030000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr11:4027200-4028600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:4027200-4029000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr11:4027200-4029200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr11:4027200-4029200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:4027200-4029200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr11:4027200-4029200	Enhancers	Psoas Muscle	Psoas
23	chr11:4027200-4030000	Enhancers	Fetal Muscle Leg	muscle
24	chr11:4027600-4029000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:4027800-4029200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr11:4028400-4028800	Enhancers	HSMMtube	muscle
27	chr11:4028400-4029800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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