Variant report

Variant	rs12989200
Chromosome Location	chr2:40577714-40577715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10165271	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10168748	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10178405	0.90[CHB][hapmap]
rs10192546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124739	0.86[ASN][1000 genomes]
rs11690171	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12468092	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12611602	0.84[CEU][hapmap]
rs12712692	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12987979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12988856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12989852	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12995004	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13014950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13017968	0.85[CHB][hapmap]
rs13022231	0.85[CHB][hapmap]
rs13031340	0.80[CHB][hapmap]
rs13031441	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs13405065	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1477004	0.85[CHB][hapmap]
rs1558654	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1558655	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2192779	0.81[CHB][hapmap]
rs2373857	0.89[CHB][hapmap]
rs4446101	0.95[CHB][hapmap]
rs4645043	0.90[CHB][hapmap]
rs4952409	0.84[CHB][hapmap]
rs6544323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs6544324	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544325	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6544326	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544329	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544330	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544334	0.85[CHB][hapmap]
rs6709574	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6738580	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6738673	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs967351	0.84[CHB][hapmap]
rs981739	0.90[CHB][hapmap]
rs984707	0.85[CHB][hapmap]
rs990270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	nsv1010508	chr2:40526981-40590777	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv535655	chr2:40526981-40590777	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv873914	chr2:40573350-40586022	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv516330	chr2:40576347-40579948	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40543200-40578800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40552800-40590600	Weak transcription	Fetal Kidney	kidney
3	chr2:40560200-40579000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:40571600-40582600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:40574000-40579600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:40574600-40579400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:40574600-40579600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:40574600-40580000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:40574600-40580000	Weak transcription	Left Ventricle	heart
10	chr2:40574600-40586000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:40574600-40590600	Weak transcription	Aorta	Aorta
12	chr2:40574800-40579600	Weak transcription	Dnd41	blood
13	chr2:40576000-40578400	Weak transcription	Hela-S3	cervix
14	chr2:40576000-40579800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:40576000-40579800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:40576200-40578800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:40576400-40578800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:40576400-40579800	Weak transcription	Right Ventricle	heart
19	chr2:40576600-40578800	Weak transcription	HSMMtube	muscle
20	chr2:40576600-40579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:40576800-40578400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:40576800-40578400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:40576800-40578400	Weak transcription	NHDF-Ad	bronchial
24	chr2:40576800-40578600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:40576800-40578600	Weak transcription	Fetal Heart	heart
26	chr2:40576800-40578600	Weak transcription	Osteobl	bone
27	chr2:40576800-40578800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:40576800-40578800	Weak transcription	HMEC	breast
29	chr2:40576800-40579200	Weak transcription	NHLF	lung
30	chr2:40576800-40579800	Weak transcription	Right Atrium	heart
31	chr2:40576800-40587600	Weak transcription	NH-A	brain
32	chr2:40577600-40578200	Weak transcription	HSMM	muscle
33	chr2:40577600-40578400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:40577600-40579800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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