Variant report

Variant	rs1641454
Chromosome Location	chr2:40446261-40446262
allele	A/C
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	POLR2A	chr2:40445795-40446265	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr2:40445861-40446338	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
SLC8A1-AS1	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1012311	0.82[EUR][1000 genomes]
rs10197174	0.82[EUR][1000 genomes]
rs107008	0.87[ASN][1000 genomes]
rs12612349	0.83[EUR][1000 genomes]
rs12993486	0.80[ASN][1000 genomes]
rs1617492	0.82[ASN][1000 genomes]
rs1641453	0.92[ASN][1000 genomes]
rs1651354	0.81[ASN][1000 genomes]
rs17025380	0.80[ASN][1000 genomes]
rs2540904	0.97[ASN][1000 genomes]
rs367596	0.97[ASN][1000 genomes]
rs371492	0.97[ASN][1000 genomes]
rs373273	0.96[ASN][1000 genomes]
rs376303	0.95[ASN][1000 genomes]
rs376535	0.81[ASN][1000 genomes]
rs379804	0.82[ASN][1000 genomes]
rs380590	0.86[EUR][1000 genomes]
rs384673	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs385665	0.80[ASN][1000 genomes]
rs386984	0.88[ASN][1000 genomes]
rs388467	0.81[ASN][1000 genomes]
rs390145	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392317	0.85[EUR][1000 genomes]
rs392953	0.98[ASN][1000 genomes]
rs395755	0.94[ASN][1000 genomes]
rs395987	0.81[ASN][1000 genomes]
rs398898	0.82[ASN][1000 genomes]
rs402777	0.81[ASN][1000 genomes]
rs404214	0.96[ASN][1000 genomes]
rs404226	0.97[ASN][1000 genomes]
rs407148	0.97[ASN][1000 genomes]
rs408263	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs410912	0.82[ASN][1000 genomes]
rs419125	0.94[ASN][1000 genomes]
rs426140	0.81[ASN][1000 genomes]
rs435404	0.87[ASN][1000 genomes]
rs436245	0.88[ASN][1000 genomes]
rs447136	0.98[ASN][1000 genomes]
rs450450	0.95[ASN][1000 genomes]
rs473400	0.95[ASN][1000 genomes]
rs481800	0.93[ASN][1000 genomes]
rs530048	0.98[ASN][1000 genomes]
rs60592471	0.85[ASN][1000 genomes]
rs62148799	0.98[ASN][1000 genomes]
rs66950674	0.84[ASN][1000 genomes]
rs6706969	0.97[ASN][1000 genomes]
rs671010	0.95[ASN][1000 genomes]
rs6757136	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv526425	chr2:40418386-40447587	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv526074	chr2:40423454-40451724	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40418200-40447200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40437200-40453200	Weak transcription	Right Ventricle	heart
3	chr2:40438000-40447200	Weak transcription	Fetal Brain Male	brain
4	chr2:40440600-40447400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:40441600-40447400	Weak transcription	Left Ventricle	heart
6	chr2:40445000-40446400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr2:40445000-40447400	Weak transcription	NHLF	lung
8	chr2:40445200-40448200	Enhancers	Fetal Heart	heart
9	chr2:40445600-40446600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:40445600-40448200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:40445800-40446400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:40445800-40446400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:40445800-40446400	Enhancers	Adipose Nuclei	Adipose
14	chr2:40445800-40446400	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:40445800-40446400	Enhancers	Ovary	ovary
16	chr2:40445800-40446400	Enhancers	HMEC	breast
17	chr2:40445800-40446600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:40445800-40446600	Enhancers	Fetal Lung	lung
19	chr2:40445800-40446600	Enhancers	Fetal Stomach	stomach
20	chr2:40445800-40446600	Enhancers	Dnd41	blood
21	chr2:40445800-40447800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:40445800-40447800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr2:40445800-40448000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:40445800-40448200	Enhancers	Colon Smooth Muscle	Colon
25	chr2:40446000-40446400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:40446000-40446400	Enhancers	Fetal Intestine Large	intestine
27	chr2:40446000-40446400	Enhancers	Fetal Muscle Leg	muscle
28	chr2:40446000-40446400	Enhancers	Right Atrium	heart
29	chr2:40446000-40446600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:40446000-40446600	Enhancers	Rectal Smooth Muscle	rectum
31	chr2:40446000-40446800	Enhancers	Stomach Smooth Muscle	stomach
32	chr2:40446000-40447600	Enhancers	HSMMtube	muscle
33	chr2:40446000-40448000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:40446000-40448000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:40446000-40448000	Enhancers	Osteobl	bone
36	chr2:40446000-40448200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr2:40446000-40448200	Enhancers	HSMM	muscle
38	chr2:40446200-40446400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr2:40446200-40447200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:40446200-40447400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:40446200-40447400	Weak transcription	Brain Germinal Matrix	brain
42	chr2:40446200-40447400	Weak transcription	Fetal Kidney	kidney
43	chr2:40446200-40447400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:40446200-40448000	Enhancers	NHDF-Ad	bronchial

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