Variant report

Variant	rs6545417
Chromosome Location	chr2:54732214-54732215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54727594..54730058-chr2:54731900..54733434,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10169013	1.00[ASN][1000 genomes]
rs10171393	1.00[ASN][1000 genomes]
rs10172671	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182310	1.00[ASN][1000 genomes]
rs10188548	1.00[ASN][1000 genomes]
rs10189084	1.00[ASN][1000 genomes]
rs10191357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194488	1.00[ASN][1000 genomes]
rs10195423	1.00[ASN][1000 genomes]
rs10206622	1.00[ASN][1000 genomes]
rs13391762	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403817	1.00[ASN][1000 genomes]
rs13414727	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs13415413	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415949	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13423872	1.00[ASN][1000 genomes]
rs13425620	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426037	1.00[ASN][1000 genomes]
rs13427468	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428524	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431302	1.00[ASN][1000 genomes]
rs17045949	1.00[ASN][1000 genomes]
rs2229505	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28496426	1.00[ASN][1000 genomes]
rs28609649	1.00[ASN][1000 genomes]
rs28660202	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28679552	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4387841	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6545426	1.00[ASN][1000 genomes]
rs6735962	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746379	1.00[ASN][1000 genomes]
rs7340250	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73934326	1.00[ASN][1000 genomes]
rs7574433	1.00[ASN][1000 genomes]
rs9808516	1.00[EUR][1000 genomes];1.00[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	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002611	chr2:54718022-54752839	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv518406	chr2:54723271-54761329	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54712400-54737000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:54717800-54732800	Enhancers	Brain Anterior Caudate	brain
3	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
4	chr2:54723800-54732600	Enhancers	Fetal Heart	heart
5	chr2:54723800-54733000	Enhancers	Adipose Nuclei	Adipose
6	chr2:54724200-54732800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54724200-54732800	Enhancers	Brain Cingulate Gyrus	brain
8	chr2:54724400-54732800	Enhancers	Brain Hippocampus Middle	brain
9	chr2:54724600-54732800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:54725000-54733000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:54725200-54737600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:54725600-54732600	Weak transcription	Small Intestine	intestine
13	chr2:54725800-54732800	Enhancers	NHDF-Ad	bronchial
14	chr2:54726000-54733000	Enhancers	Brain Angular Gyrus	brain
15	chr2:54726400-54740000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:54726400-54740000	Weak transcription	Pancreas	Pancrea
17	chr2:54726600-54733000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr2:54727400-54732400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:54727600-54737800	Weak transcription	A549	lung
20	chr2:54728000-54732800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:54728000-54737400	Weak transcription	HSMM	muscle
22	chr2:54728200-54732600	Enhancers	Rectal Smooth Muscle	rectum
23	chr2:54728400-54732600	Weak transcription	Fetal Intestine Small	intestine
24	chr2:54729000-54732800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:54729000-54733400	Weak transcription	Gastric	stomach
26	chr2:54729600-54732400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:54729800-54732800	Enhancers	NHLF	lung
28	chr2:54730000-54739400	Weak transcription	Fetal Brain Female	brain
29	chr2:54730200-54732800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:54730200-54735400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:54730200-54736800	Weak transcription	Placenta	Placenta
32	chr2:54730400-54732800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:54730400-54736800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:54730600-54732600	Weak transcription	Left Ventricle	heart
36	chr2:54730600-54732600	Weak transcription	Lung	lung
37	chr2:54730600-54735600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:54730600-54736600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:54730600-54739000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:54730600-54739200	Weak transcription	Spleen	Spleen
41	chr2:54730600-54739400	Weak transcription	HepG2	liver
42	chr2:54730600-54740000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:54730800-54732600	Weak transcription	Right Ventricle	heart
44	chr2:54730800-54734600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:54730800-54736800	Weak transcription	Fetal Brain Male	brain
46	chr2:54730800-54738600	Enhancers	Fetal Lung	lung
47	chr2:54731200-54737400	Weak transcription	Fetal Stomach	stomach
48	chr2:54731400-54732400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:54731400-54732400	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:54731400-54732400	Enhancers	HSMMtube	muscle

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