Variant report

Variant	rs55954817
Chromosome Location	chr3:28314844-28314845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10510607	0.90[ASN][1000 genomes]
rs10510609	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12054402	0.82[ASN][1000 genomes]
rs17021298	0.92[ASN][1000 genomes]
rs4502545	0.92[ASN][1000 genomes]
rs4680906	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56029590	0.92[ASN][1000 genomes]
rs56085195	0.92[ASN][1000 genomes]
rs56116734	0.82[ASN][1000 genomes]
rs7645825	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28284000-28317200	Weak transcription	Gastric	stomach
2	chr3:28284400-28321800	Weak transcription	NHLF	lung
3	chr3:28285600-28315400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:28287600-28317000	Weak transcription	Pancreas	Pancrea
5	chr3:28294800-28316400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:28295600-28318200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:28303000-28316800	Weak transcription	Right Ventricle	heart
8	chr3:28303400-28322200	Weak transcription	Small Intestine	intestine
9	chr3:28303600-28340600	Weak transcription	NHEK	skin
10	chr3:28303800-28320800	Weak transcription	Placenta	Placenta
11	chr3:28304200-28332400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:28305600-28322600	Weak transcription	Osteobl	bone
13	chr3:28306200-28316600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:28306400-28332400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:28306600-28335800	Weak transcription	Hela-S3	cervix
16	chr3:28307400-28317400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:28307600-28317000	Weak transcription	Fetal Thymus	thymus
18	chr3:28308600-28315200	Weak transcription	K562	blood
19	chr3:28309000-28336600	Weak transcription	HUVEC	blood vessel
20	chr3:28309400-28317000	Weak transcription	HSMM	muscle
21	chr3:28309600-28317000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:28310000-28317000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:28310400-28321200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:28311000-28315600	ZNF genes & repeats	Dnd41	blood
25	chr3:28311200-28317200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:28311400-28319000	Weak transcription	Spleen	Spleen
27	chr3:28311600-28317000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:28311600-28317000	Weak transcription	Aorta	Aorta
29	chr3:28311600-28317000	Weak transcription	Esophagus	oesophagus
30	chr3:28311600-28319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:28312600-28315000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:28312600-28316800	ZNF genes & repeats	Fetal Lung	lung
33	chr3:28313000-28315800	Strong transcription	Fetal Kidney	kidney
34	chr3:28313400-28315200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:28313400-28322800	Weak transcription	Colonic Mucosa	Colon
36	chr3:28313600-28315600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:28313600-28315600	ZNF genes & repeats	Liver	Liver
38	chr3:28313600-28315800	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr3:28313600-28316200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:28313600-28316200	ZNF genes & repeats	Fetal Intestine Large	intestine
41	chr3:28313600-28316400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:28313800-28315000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:28313800-28315000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
44	chr3:28313800-28315000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
45	chr3:28313800-28315200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
46	chr3:28313800-28315600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
47	chr3:28313800-28315600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
48	chr3:28313800-28315600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
49	chr3:28313800-28315800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:28313800-28316000	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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