Variant report

Variant	rs55997345
Chromosome Location	chr3:196218353-196218354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196217384..196220368-chr3:196221757..196224156,3	K562	blood:
2	chr3:196209607..196212494-chr3:196216409..196218817,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11185543	0.89[ASN][1000 genomes]
rs11707744	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718980	0.89[ASN][1000 genomes]
rs11719920	0.87[ASN][1000 genomes]
rs12632592	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635457	0.90[ASN][1000 genomes]
rs13084212	0.89[ASN][1000 genomes]
rs13098146	0.87[ASN][1000 genomes]
rs13099664	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34196595	0.88[ASN][1000 genomes]
rs34547573	0.80[EUR][1000 genomes]
rs34722299	0.80[ASN][1000 genomes]
rs3796129	0.87[ASN][1000 genomes]
rs4244200	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4393941	0.87[ASN][1000 genomes]
rs4916431	0.87[ASN][1000 genomes]
rs4916497	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916498	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916499	0.87[ASN][1000 genomes]
rs5016648	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772271	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6775484	0.87[ASN][1000 genomes]
rs6803161	0.90[ASN][1000 genomes]
rs71630192	0.89[ASN][1000 genomes]
rs7430950	0.80[EUR][1000 genomes]
rs7433483	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611980	0.89[ASN][1000 genomes]
rs7612450	0.89[ASN][1000 genomes]
rs7643192	0.89[ASN][1000 genomes]
rs7646174	0.89[ASN][1000 genomes]
rs7646273	0.89[ASN][1000 genomes]
rs7647487	0.87[ASN][1000 genomes]
rs9843876	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9856006	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9864836	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9872866	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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	45 gene(s)	inside rSNPs	diseases
4	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv878186	chr3:196158773-196219794	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55997345	FBXO45	Cis_1M	lymphoblastoid	RTeQTL
rs55997345	UBXD7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196197000-196220000	Weak transcription	Stomach Mucosa	stomach
2	chr3:196197200-196223800	Strong transcription	Fetal Thymus	thymus
3	chr3:196199400-196227000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:196210600-196219000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:196210800-196226000	Weak transcription	Psoas Muscle	Psoas
6	chr3:196212000-196222000	Weak transcription	HSMM	muscle
7	chr3:196213000-196226800	Weak transcription	Fetal Kidney	kidney
8	chr3:196213200-196222000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:196213400-196225800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:196213800-196226600	Weak transcription	Brain Substantia Nigra	brain
11	chr3:196214200-196223000	Weak transcription	Brain Germinal Matrix	brain
12	chr3:196214200-196225000	Weak transcription	Ovary	ovary
13	chr3:196214200-196225400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:196214200-196225400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:196214200-196226000	Weak transcription	A549	lung
16	chr3:196214400-196219800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:196214400-196221400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:196214400-196221600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:196214400-196222000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:196214400-196222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:196214400-196222400	Weak transcription	HUVEC	blood vessel
22	chr3:196214400-196222600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:196214400-196222800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:196214400-196223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:196214400-196223000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:196214400-196225000	Weak transcription	Small Intestine	intestine
27	chr3:196214400-196225800	Weak transcription	HSMMtube	muscle
28	chr3:196214400-196225800	Weak transcription	NHEK	skin
29	chr3:196214400-196226000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:196214400-196226000	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:196214400-196226000	Weak transcription	Esophagus	oesophagus
32	chr3:196214400-196226000	Weak transcription	Gastric	stomach
33	chr3:196214400-196226200	Weak transcription	Right Ventricle	heart
34	chr3:196214400-196226400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:196214400-196226600	Weak transcription	Aorta	Aorta
36	chr3:196214400-196226800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:196214400-196226800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:196214400-196226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:196214400-196226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:196214400-196226800	Weak transcription	Brain Anterior Caudate	brain
41	chr3:196214400-196226800	Weak transcription	Pancreas	Pancrea
42	chr3:196214400-196227000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:196214400-196227000	Weak transcription	Fetal Lung	lung
44	chr3:196214400-196227000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:196214400-196228200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:196214600-196221400	Weak transcription	Left Ventricle	heart
47	chr3:196214600-196221600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:196214600-196222000	Weak transcription	NH-A	brain
49	chr3:196214600-196222200	Weak transcription	Adipose Nuclei	Adipose
50	chr3:196214600-196223000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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