Variant report

Variant	rs2553769
Chromosome Location	chr11:108768830-108768831
allele	A/G
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:28)

rs_ID	r²[population]
rs1466502	0.91[YRI][hapmap]
rs1469274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1531470	0.84[ASW][hapmap];0.95[GIH][hapmap];0.95[MKK][hapmap]
rs17108759	1.00[ASN][1000 genomes]
rs17703817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947928	1.00[ASW][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.88[YRI][hapmap]
rs1947929	1.00[ASW][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.88[YRI][hapmap]
rs2061680	0.88[YRI][hapmap]
rs2126570	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2615734	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2726876	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2726880	0.95[GIH][hapmap];0.94[MKK][hapmap]
rs2726887	0.92[ASW][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.88[YRI][hapmap]
rs2726905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2726924	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57196252	0.87[ASN][1000 genomes]
rs59287866	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7103209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124142	0.95[GIH][hapmap]
rs7130825	0.95[GIH][hapmap]
rs71489923	0.82[ASN][1000 genomes]
rs72993315	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72993517	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72993528	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72993554	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7931638	0.91[GIH][hapmap]
rs7944806	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv898386	chr11:108409442-108831875	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv898389	chr11:108724639-108891986	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv2761707	chr11:108763836-108772204	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108728400-108810600	Weak transcription	Left Ventricle	heart
2	chr11:108763000-108797600	Weak transcription	Fetal Muscle Leg	muscle
3	chr11:108766600-108775600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:108766800-108769800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr11:108767000-108777200	Weak transcription	Adipose Nuclei	Adipose
6	chr11:108767400-108769000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:108767600-108777000	Weak transcription	HSMM	muscle
8	chr11:108767800-108769200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:108768000-108769000	Weak transcription	A549	lung
10	chr11:108768000-108770000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:108768000-108776400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:108768000-108810600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:108768200-108771200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:108768200-108771400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:108768200-108772000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:108768200-108776400	Weak transcription	NHEK	skin
17	chr11:108768200-108777000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:108768200-108779800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:108768400-108769000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr11:108768400-108772400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr11:108768400-108772600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:108768400-108773000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:108768600-108769200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:108768600-108769800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:108768600-108769800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:108768600-108776200	Weak transcription	NH-A	brain
27	chr11:108768800-108769200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
28	chr11:108768800-108769800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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