Variant report

Variant	rs12577299
Chromosome Location	chr11:107380894-107380895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10502092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10502093	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs10890735	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10890736	0.87[EUR][1000 genomes]
rs11212269	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212271	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212275	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs11212277	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11212278	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11212279	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12224115	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12225894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12226565	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs12286285	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs12574614	0.86[EUR][1000 genomes]
rs12576309	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2037822	0.87[EUR][1000 genomes]
rs2037823	0.84[EUR][1000 genomes]
rs2037824	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2037825	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2037826	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2037827	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2141387	0.81[EUR][1000 genomes]
rs4754230	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs490312	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs490459	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs591463	0.80[CEU][hapmap]
rs61908161	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61908178	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61908179	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61908181	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61908182	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61908194	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61908195	0.86[EUR][1000 genomes]
rs61908196	0.86[EUR][1000 genomes]
rs61908197	0.83[EUR][1000 genomes]
rs61908198	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs650218	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs650669	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs659622	0.82[CHB][hapmap]
rs7109955	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs73002096	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9735734	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1038368	chr11:107116577-107664181	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv541163	chr11:107116577-107664181	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv898373	chr11:107124903-107433835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv556376	chr11:107250851-107486598	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv898376	chr11:107299631-107443420	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107364000-107394000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:107367200-107387400	Weak transcription	Fetal Heart	heart
3	chr11:107369200-107406400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:107370000-107433800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:107371000-107383200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:107371200-107393000	Weak transcription	Brain Substantia Nigra	brain
7	chr11:107371200-107421200	Weak transcription	Right Ventricle	heart
8	chr11:107372000-107435600	Weak transcription	Colonic Mucosa	Colon
9	chr11:107372800-107389600	Weak transcription	Gastric	stomach
10	chr11:107372800-107409600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:107372800-107434600	Weak transcription	Placenta	Placenta
12	chr11:107373000-107386200	Weak transcription	Pancreas	Pancrea
13	chr11:107373000-107414800	Weak transcription	Brain Anterior Caudate	brain
14	chr11:107373000-107415200	Weak transcription	Osteobl	bone
15	chr11:107373000-107421000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:107373000-107421400	Weak transcription	Brain Germinal Matrix	brain
17	chr11:107373200-107384400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:107373200-107384400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:107373200-107389000	Weak transcription	Fetal Intestine Small	intestine
20	chr11:107373200-107389600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:107373200-107390800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:107373200-107393000	Weak transcription	Fetal Stomach	stomach
23	chr11:107373200-107396200	Weak transcription	Small Intestine	intestine
24	chr11:107373200-107405800	Weak transcription	NHEK	skin
25	chr11:107373200-107407400	Weak transcription	Esophagus	oesophagus
26	chr11:107373200-107421000	Weak transcription	Spleen	Spleen
27	chr11:107373200-107423200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:107373400-107407400	Weak transcription	GM12878-XiMat	blood
29	chr11:107373800-107381400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:107373800-107409200	Weak transcription	HepG2	liver
31	chr11:107375600-107389000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:107375600-107393000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:107375600-107414600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:107375800-107381200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:107375800-107381200	Weak transcription	NHDF-Ad	bronchial
36	chr11:107375800-107384400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:107375800-107388200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:107375800-107388200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:107375800-107388400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:107375800-107389600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:107375800-107390000	Weak transcription	HUVEC	blood vessel
42	chr11:107375800-107390800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:107375800-107392200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:107375800-107392800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:107375800-107393000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr11:107375800-107395800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr11:107375800-107396800	Weak transcription	HSMM	muscle
48	chr11:107375800-107402400	Weak transcription	Fetal Thymus	thymus
49	chr11:107375800-107407000	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:107376000-107381200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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