Variant report

Variant	rs1546542
Chromosome Location	chr11:9900458-9900459
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12099354	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12360818	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12365540	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12365901	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12796169	0.83[ASW][hapmap];0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1546541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17354870	0.82[JPT][hapmap]
rs2017503	0.85[AFR][1000 genomes]
rs35396321	0.90[EUR][1000 genomes]
rs35749184	0.83[AFR][1000 genomes]
rs4334006	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4445629	0.85[EUR][1000 genomes]
rs4498988	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4910067	0.82[ASW][hapmap]
rs4910069	0.98[ASN][1000 genomes]
rs4910076	0.93[CEU][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6483811	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67701335	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107328	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7122293	0.82[ASW][hapmap];0.80[LWK][hapmap];0.81[AFR][1000 genomes]
rs7126063	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7131516	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7350496	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925651	0.81[EUR][1000 genomes]
rs7929338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930281	0.83[ASW][hapmap];0.89[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7948688	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9919605	0.83[ASW][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9919609	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9919617	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878400-9916200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
3	chr11:9880200-9913200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:9880600-9914800	Weak transcription	Placenta	Placenta
5	chr11:9880800-9902200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
7	chr11:9884800-9905400	Weak transcription	NHLF	lung
8	chr11:9885800-9905600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:9890600-9915200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:9891400-9916800	Weak transcription	Primary B cells from cord blood	blood
11	chr11:9891600-9902000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:9891800-9916600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:9892200-9914600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:9892400-9914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:9892400-9914600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr11:9892400-9921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:9894000-9910600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:9894200-9915200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr11:9894400-9903200	Weak transcription	A549	lung
20	chr11:9894400-9907400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:9894400-9916600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
23	chr11:9897000-9915000	Weak transcription	HSMMtube	muscle
24	chr11:9897200-9902400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:9897400-9909000	Weak transcription	Psoas Muscle	Psoas
26	chr11:9897800-9903200	Weak transcription	Fetal Lung	lung
27	chr11:9897800-9910000	Weak transcription	Fetal Kidney	kidney
28	chr11:9898200-9903000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:9898200-9914800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:9898200-9917000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:9898400-9913800	Weak transcription	Fetal Stomach	stomach
32	chr11:9898600-9914800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:9898800-9915200	Weak transcription	Fetal Intestine Small	intestine
34	chr11:9899400-9915000	Weak transcription	Liver	Liver
35	chr11:9900000-9903600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:9900200-9900600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr11:9900400-9900600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr11:9900400-9900600	Enhancers	NHDF-Ad	bronchial
39	chr11:9900400-9900800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr11:9900400-9901600	Enhancers	Ovary	ovary

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