Variant report

Variant	rs2299057
Chromosome Location	chr6:15377528-15377529
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15210646..15214635-chr6:15377351..15380909,4	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10484355	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10949294	0.83[ASN][1000 genomes]
rs10949295	0.83[ASN][1000 genomes]
rs11756544	0.95[ASN][1000 genomes]
rs11757415	0.95[ASN][1000 genomes]
rs12211278	0.83[ASN][1000 genomes]
rs13192347	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194410	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13195950	0.95[ASN][1000 genomes]
rs13205396	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205612	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208486	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13214720	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16876278	0.83[ASN][1000 genomes]
rs16876354	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17576233	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17576436	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17576710	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17637773	0.83[ASN][1000 genomes]
rs17638192	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17638720	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237146	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299051	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34002211	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34764533	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35047303	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35139070	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364784	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35629999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35734069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35918625	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56123857	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56265026	0.83[ASN][1000 genomes]
rs61296041	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66478504	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6941859	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72836327	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7747437	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7767966	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15341800-15378400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:15364600-15390200	Weak transcription	HepG2	liver
3	chr6:15365000-15402800	Weak transcription	Dnd41	blood
4	chr6:15365800-15378600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:15365800-15384800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:15366400-15382600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:15366600-15378600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:15366600-15384800	Weak transcription	NH-A	brain
9	chr6:15366600-15385000	Weak transcription	Fetal Brain Female	brain
10	chr6:15367000-15379200	Weak transcription	Brain Germinal Matrix	brain
11	chr6:15367000-15384800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:15367400-15384600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:15367400-15389400	Weak transcription	Ovary	ovary
14	chr6:15370200-15381600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:15370200-15381600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:15370400-15378800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:15370400-15379400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:15370400-15383000	Weak transcription	Spleen	Spleen
19	chr6:15370400-15384800	Weak transcription	Pancreas	Pancrea
20	chr6:15371200-15384800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:15371600-15382600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:15371800-15381800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:15371800-15389000	Weak transcription	Adipose Nuclei	Adipose
24	chr6:15372000-15386600	Weak transcription	Fetal Intestine Small	intestine
25	chr6:15372200-15378600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:15372200-15379200	Weak transcription	Brain Anterior Caudate	brain
27	chr6:15372400-15379400	Weak transcription	Fetal Lung	lung
28	chr6:15372800-15377600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:15373600-15377600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr6:15373800-15379200	Strong transcription	Primary B cells from cord blood	blood
31	chr6:15374000-15380000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr6:15374200-15377800	Strong transcription	Thymus	Thymus
33	chr6:15374200-15389200	Weak transcription	HSMM	muscle
34	chr6:15374400-15378200	Strong transcription	GM12878-XiMat	blood
35	chr6:15374600-15378200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:15374600-15378200	Strong transcription	Fetal Thymus	thymus
37	chr6:15374600-15378400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:15374600-15378600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:15374600-15385000	Weak transcription	Small Intestine	intestine
40	chr6:15375000-15377600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:15375000-15378000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:15375000-15378400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:15375000-15378600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:15375000-15379200	Weak transcription	Right Ventricle	heart
45	chr6:15375000-15383000	Weak transcription	HMEC	breast
46	chr6:15375000-15383200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:15375000-15385000	Weak transcription	Fetal Kidney	kidney
48	chr6:15375400-15380600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr6:15375600-15377600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:15375600-15377800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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