Variant report

Variant	rs2959058
Chromosome Location	chr11:4001008-4001009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3996537..3998717-chr11:4000527..4002843,2	K562	blood:
2	chr11:3996537..3998429-chr11:4000014..4002027,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10734400	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742194	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10742207	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767775	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835333	0.81[LWK][hapmap]
rs10835500	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11030584	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11602757	0.86[MKK][hapmap]
rs1465952	0.91[LWK][hapmap];0.85[MKK][hapmap]
rs2289570	0.93[LWK][hapmap];0.90[MKK][hapmap]
rs2860454	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2898950	0.98[LWK][hapmap];0.90[MKK][hapmap]
rs2923946	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923958	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923959	0.82[AFR][1000 genomes]
rs2959059	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959080	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]
rs4379839	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910588	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910595	0.95[LWK][hapmap];0.86[MKK][hapmap]
rs6578430	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs727152	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928763	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945918	0.91[LWK][hapmap];0.86[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	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2959058	DCHS1	cis	parietal	SCAN
rs2959058	TRIM21	cis	cerebellum	SCAN
rs2959058	RRM1	cis	cerebellum	SCAN
rs2959058	KRTAP5-4	cis	cerebellum	SCAN
rs2959058	ANO9	cis	parietal	SCAN
rs2959058	IFITM5	cis	cerebellum	SCAN
rs2959058	C11orf21	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
3	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
4	chr11:3982600-4004400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:3982600-4005600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:3982600-4006000	Weak transcription	Left Ventricle	heart
7	chr11:3984000-4010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:3985000-4002400	Weak transcription	NHDF-Ad	bronchial
9	chr11:3985800-4001200	Weak transcription	Small Intestine	intestine
10	chr11:3986000-4008000	Weak transcription	HepG2	liver
11	chr11:3987000-4010400	Weak transcription	Fetal Intestine Small	intestine
12	chr11:3987200-4001600	Weak transcription	Gastric	stomach
13	chr11:3988000-4002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:3988200-4006200	Weak transcription	Pancreas	Pancrea
15	chr11:3989400-4010600	Weak transcription	Spleen	Spleen
16	chr11:3989400-4031000	Weak transcription	Aorta	Aorta
17	chr11:3989800-4002400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:3989800-4006000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:3989800-4006200	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:3989800-4006600	Weak transcription	Liver	Liver
21	chr11:3990000-4002000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:3990400-4006000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:3991200-4002400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:3991200-4004400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:3991200-4006200	Weak transcription	Adipose Nuclei	Adipose
26	chr11:3991400-4003000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:3991600-4002800	Weak transcription	Dnd41	blood
28	chr11:3991600-4003800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:3991600-4004400	Weak transcription	GM12878-XiMat	blood
30	chr11:3993200-4003800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr11:3993800-4003600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:3994400-4016600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:3994600-4002000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:3994600-4002400	Weak transcription	Esophagus	oesophagus
35	chr11:3994600-4002400	Weak transcription	Thymus	Thymus
36	chr11:3995400-4004200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:3995400-4005800	Weak transcription	Fetal Stomach	stomach
38	chr11:3996800-4002200	Weak transcription	Psoas Muscle	Psoas
39	chr11:3997000-4004800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr11:3997200-4004800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:3998600-4008800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr11:3998800-4001200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr11:3999200-4004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr11:3999400-4001200	Weak transcription	K562	blood
45	chr11:3999800-4001400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr11:4000000-4001400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr11:4000200-4001200	Weak transcription	Stomach Mucosa	stomach
48	chr11:4000600-4001800	Strong transcription	Primary B cells from cord blood	blood
49	chr11:4000600-4002200	Weak transcription	Primary T cells from cord blood	blood
50	chr11:4000600-4002800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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