Variant report

Variant	rs2923946
Chromosome Location	chr11:4011806-4011807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10734400	1.00[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];0.98[ASN][1000 genomes]
rs10742194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10742207	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767775	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835500	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11030584	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11602757	0.90[GIH][hapmap];0.88[MKK][hapmap]
rs1465952	0.93[LWK][hapmap];0.94[MKK][hapmap]
rs2289570	0.90[GIH][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap]
rs2860454	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2898950	0.90[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap]
rs2920137	0.90[GIH][hapmap]
rs2920142	0.90[GIH][hapmap]
rs2923958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2923959	0.89[AFR][1000 genomes]
rs2959058	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]
rs2959059	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959080	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]
rs4379839	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910595	0.90[GIH][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap]
rs6578430	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs727152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[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];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928763	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945918	0.93[LWK][hapmap];0.96[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv971974	chr11:4009259-4018790	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2923946	DCHS1	cis	parietal	SCAN
rs2923946	C11orf21	cis	parietal	SCAN
rs2923946	RRM1	cis	cerebellum	SCAN
rs2923946	ANO9	cis	parietal	SCAN
rs2923946	KRTAP5-4	cis	cerebellum	SCAN
rs2923946	IFITM5	cis	cerebellum	SCAN
rs2923946	TRIM21	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3989400-4031000	Weak transcription	Aorta	Aorta
2	chr11:3994400-4016600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:4003200-4016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:4006200-4013800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr11:4006400-4016600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:4006800-4022600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:4007000-4012600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:4007200-4013800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:4007200-4014000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:4007800-4015000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:4008600-4015400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr11:4009000-4013800	Weak transcription	Primary B cells from cord blood	blood
13	chr11:4009400-4012400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:4009400-4012400	Weak transcription	Psoas Muscle	Psoas
15	chr11:4009400-4017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:4009400-4020200	Weak transcription	Pancreas	Pancrea
17	chr11:4009600-4017200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:4010000-4012000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:4010000-4012800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr11:4010800-4012000	Enhancers	Primary T cells from cord blood	blood
21	chr11:4010800-4015800	Weak transcription	Left Ventricle	heart
22	chr11:4010800-4015800	Weak transcription	Thymus	Thymus
23	chr11:4010800-4017200	Weak transcription	Fetal Thymus	thymus
24	chr11:4011000-4012400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:4011000-4012400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:4011000-4012400	Weak transcription	Fetal Stomach	stomach
27	chr11:4011000-4012400	Weak transcription	Ovary	ovary
28	chr11:4011200-4012400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr11:4011200-4014400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr11:4011200-4014400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:4011400-4013200	Weak transcription	A549	lung
32	chr11:4011600-4012800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr11:4011600-4015000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr11:4011800-4012200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr11:4011800-4012600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:4011800-4012800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr11:4011800-4013800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:4011800-4014000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:4011800-4014000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:4011800-4027600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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