Variant report

Variant	rs12998614
Chromosome Location	chr2:40682775-40682776
allele	C/T
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	CEBPB	chr2:40682517-40682865	Hela-S3	cervix:	n/a	chr2:40682690-40682701
2	CEBPB	chr2:40682553-40682823	A549	lung:	n/a	chr2:40682690-40682701
3	SPI1	chr2:40682715-40683208	HL-60	blood:	n/a	chr2:40683080-40683087
4	EBF1	chr2:40682743-40683076	GM12878	blood:	n/a	chr2:40682890-40682901 chr2:40682891-40682900

Variant related genes	Relation type
SLC8A1	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12466482	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12470186	0.97[ASN][1000 genomes]
rs12998011	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2373862	0.91[ASN][1000 genomes]
rs2373863	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2373864	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2888679	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33992047	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35732522	0.89[ASN][1000 genomes]
rs4952630	0.83[ASN][1000 genomes]
rs55742439	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56307721	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62149443	0.99[ASN][1000 genomes]
rs6544340	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728108	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6735424	0.81[EUR][1000 genomes]
rs7597373	0.82[ASN][1000 genomes]
rs767154	0.89[AMR][1000 genomes];0.96[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	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	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
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv2700	chr2:40667461-40712805	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40679800-40682800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40679800-40682800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:40679800-40685600	Weak transcription	Right Ventricle	heart
4	chr2:40680000-40682800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:40680000-40683800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:40680000-40684200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:40680000-40684200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:40680000-40684400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:40680000-40684400	Weak transcription	HSMM	muscle
10	chr2:40680000-40684600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:40680000-40685600	Weak transcription	Fetal Kidney	kidney
12	chr2:40680200-40682800	Weak transcription	HMEC	breast
13	chr2:40680200-40682800	Weak transcription	NHLF	lung
14	chr2:40680200-40684200	Weak transcription	Osteobl	bone
15	chr2:40680200-40685200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:40680800-40685000	Weak transcription	Right Atrium	heart
17	chr2:40681000-40682800	Weak transcription	Left Ventricle	heart
18	chr2:40681000-40683200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr2:40681400-40684400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:40682000-40683000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr2:40682200-40683000	Enhancers	Colon Smooth Muscle	Colon
22	chr2:40682200-40684400	Enhancers	Fetal Heart	heart
23	chr2:40682200-40684600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:40682200-40685600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:40682400-40682800	Enhancers	Primary hematopoietic stem cells	blood
26	chr2:40682600-40683000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:40682600-40683200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr2:40682600-40683200	Enhancers	Primary B cells from cord blood	blood
29	chr2:40682600-40683200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:40682600-40683200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:40682600-40683200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:40682600-40683200	Enhancers	NHDF-Ad	bronchial

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