Variant report

Variant	rs16823361
Chromosome Location	chr2:144711507-144711508
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:144711206-144711535	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GTDC1	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12612842	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613814	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12614766	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12618509	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621041	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823382	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs16823481	0.89[CHB][hapmap]
rs16823487	0.89[CHB][hapmap]
rs1861878	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1864245	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2111671	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs28679451	0.86[ASN][1000 genomes]
rs35790422	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820756	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs55634187	0.88[ASN][1000 genomes]
rs56090763	0.85[ASN][1000 genomes]
rs56120346	0.86[ASN][1000 genomes]
rs56123489	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56136411	0.85[ASN][1000 genomes]
rs56166856	0.86[ASN][1000 genomes]
rs58186643	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60305932	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61202373	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72851896	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852907	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852908	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852911	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852913	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852918	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852924	0.99[ASN][1000 genomes]
rs72852926	0.88[ASN][1000 genomes]
rs72852929	0.88[ASN][1000 genomes]
rs72852930	0.88[ASN][1000 genomes]
rs72852932	0.88[ASN][1000 genomes]
rs72852936	0.88[ASN][1000 genomes]
rs72852938	0.88[ASN][1000 genomes]
rs72852941	0.88[ASN][1000 genomes]
rs72852947	0.88[ASN][1000 genomes]
rs72852948	0.88[ASN][1000 genomes]
rs72852967	0.86[ASN][1000 genomes]
rs72852969	0.86[ASN][1000 genomes]
rs72852985	0.86[ASN][1000 genomes]
rs73962160	0.88[ASN][1000 genomes]
rs7572132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787170	0.89[ASN][1000 genomes]
rs9678811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.97[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	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144695400-144714200	Weak transcription	Gastric	stomach
2	chr2:144696000-144713200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:144696600-144712600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:144696600-144717800	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:144699600-144730400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:144700800-144719600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:144704400-144713400	Weak transcription	Esophagus	oesophagus
8	chr2:144704600-144713400	Weak transcription	Lung	lung
9	chr2:144704600-144728800	Weak transcription	Spleen	Spleen
10	chr2:144704800-144712600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:144704800-144712600	Weak transcription	Fetal Stomach	stomach
12	chr2:144704800-144713200	Weak transcription	Liver	Liver
13	chr2:144704800-144719200	Weak transcription	Primary B cells from cord blood	blood
14	chr2:144704800-144730800	Weak transcription	Left Ventricle	heart
15	chr2:144705000-144717800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:144707200-144712600	Weak transcription	Fetal Heart	heart
17	chr2:144707200-144713200	Enhancers	Fetal Brain Male	brain
18	chr2:144707400-144712000	Weak transcription	NH-A	brain
19	chr2:144708000-144713000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:144709200-144714600	Weak transcription	Fetal Kidney	kidney
21	chr2:144709400-144711800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr2:144710400-144712000	Active TSS	Ovary	ovary
23	chr2:144710600-144711800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr2:144710800-144711600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:144710800-144711800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr2:144710800-144713600	Enhancers	Osteobl	bone
27	chr2:144711000-144711600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr2:144711000-144711600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr2:144711000-144711600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr2:144711000-144711800	Enhancers	Colon Smooth Muscle	Colon
31	chr2:144711000-144711800	Enhancers	HSMMtube	muscle
32	chr2:144711000-144712000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:144711000-144713400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:144711000-144713600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:144711000-144713800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:144711200-144711800	Enhancers	Brain Hippocampus Middle	brain
37	chr2:144711200-144713800	Enhancers	HSMM	muscle
38	chr2:144711400-144711800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:144711400-144711800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr2:144711400-144712400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:144711400-144712800	Enhancers	NHDF-Ad	bronchial
42	chr2:144711400-144713000	Weak transcription	Fetal Brain Female	brain
43	chr2:144711400-144713200	Enhancers	Fetal Lung	lung
44	chr2:144711400-144713600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:144711400-144713800	Enhancers	NHLF	lung
46	chr2:144711400-144717600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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