Variant report

Variant	rs12419399
Chromosome Location	chr11:57792102-57792103
allele	C/T
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]
rs11229185	0.91[ASN][1000 genomes]
rs12291403	0.88[ASN][1000 genomes]
rs12417244	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12417258	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12417892	0.91[ASN][1000 genomes]
rs12418547	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12419044	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12419348	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12419513	0.80[ASN][1000 genomes]
rs12420912	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12575698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397277	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1868882	1.00[CEU][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2441965	1.00[CEU][hapmap]
rs2441968	0.83[JPT][hapmap]
rs2441976	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs2441983	1.00[CEU][hapmap]
rs2443448	1.00[CEU][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs2513706	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2513724	1.00[CEU][hapmap]
rs2514182	0.83[JPT][hapmap]
rs2514190	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2514192	1.00[CEU][hapmap]
rs2514207	0.83[JPT][hapmap]
rs2514209	0.82[JPT][hapmap]
rs3974333	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7120194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs986053	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv2761678	chr11:57768288-57810886	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	5 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	chr11:57787800-57794600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:57790200-57792600	Enhancers	Rectal Mucosa Donor 29	rectum
3	chr11:57790200-57792800	Enhancers	Fetal Muscle Leg	muscle
4	chr11:57790800-57792800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr11:57791000-57792400	Enhancers	Fetal Lung	lung
6	chr11:57791200-57792600	Enhancers	NHLF	lung
7	chr11:57791200-57792800	Enhancers	Spleen	Spleen
8	chr11:57791200-57793200	Enhancers	Duodenum Mucosa	Duodenum
9	chr11:57791200-57798200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:57791400-57792200	Enhancers	Left Ventricle	heart
11	chr11:57791400-57792200	Enhancers	Pancreas	Pancrea
12	chr11:57791400-57792400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:57791400-57792400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr11:57791400-57792600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:57791400-57792600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr11:57791400-57792800	Enhancers	Fetal Muscle Trunk	muscle
17	chr11:57791400-57792800	Enhancers	HepG2	liver
18	chr11:57791400-57792800	Enhancers	HUVEC	blood vessel
19	chr11:57791400-57793400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:57791400-57793400	Enhancers	Psoas Muscle	Psoas
21	chr11:57791600-57792200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:57791600-57792200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr11:57791600-57792200	Enhancers	Small Intestine	intestine
24	chr11:57791600-57792200	Enhancers	Stomach Mucosa	stomach
25	chr11:57791600-57792400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:57791600-57792400	Enhancers	Esophagus	oesophagus
27	chr11:57791600-57792600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr11:57791600-57792600	Enhancers	Placenta	Placenta
29	chr11:57791600-57792600	Enhancers	HSMMtube	muscle
30	chr11:57791600-57792800	Enhancers	Lung	lung
31	chr11:57791800-57792200	Enhancers	Adipose Nuclei	Adipose
32	chr11:57791800-57792200	Flanking Active TSS	HSMM	muscle
33	chr11:57791800-57792200	Enhancers	Osteobl	bone
34	chr11:57792000-57792200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr11:57792000-57792400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:57792000-57792400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:57792000-57792400	Enhancers	Brain Germinal Matrix	brain
38	chr11:57792000-57792600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:57792000-57795400	Weak transcription	Colonic Mucosa	Colon
40	chr11:57792000-57811400	Weak transcription	Right Atrium	heart

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