Variant report

Variant	rs12408253
Chromosome Location	chr1:171156544-171156545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10912478	0.82[ASN][1000 genomes]
rs10912484	0.82[ASN][1000 genomes]
rs10912486	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912524	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11804100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11806352	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11806405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11807206	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12129672	0.82[ASN][1000 genomes]
rs12132443	0.82[ASN][1000 genomes]
rs12133379	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134777	0.82[ASN][1000 genomes]
rs12136568	0.82[ASN][1000 genomes]
rs12406402	0.82[ASN][1000 genomes]
rs12408043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729618	0.80[ASN][1000 genomes]
rs12744605	0.82[ASN][1000 genomes]
rs2205730	0.82[ASN][1000 genomes]
rs2205732	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421707	0.80[ASN][1000 genomes]
rs28369845	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28369881	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2901513	0.80[ASN][1000 genomes]
rs4916410	0.82[ASN][1000 genomes]
rs61814303	0.82[ASN][1000 genomes]
rs6608456	0.80[ASN][1000 genomes]
rs7531111	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7887295	0.82[ASN][1000 genomes]
rs7891433	0.82[ASN][1000 genomes]
rs9730437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171153400-171159000	Active TSS	Aorta	Aorta
2	chr1:171154000-171159600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:171154200-171156600	Active TSS	Stomach Smooth Muscle	stomach
4	chr1:171154200-171156600	Active TSS	NHLF	lung
5	chr1:171154200-171157400	Active TSS	Adipose Nuclei	Adipose
6	chr1:171154200-171158800	Active TSS	Psoas Muscle	Psoas
7	chr1:171154200-171159000	Active TSS	Left Ventricle	heart
8	chr1:171154200-171160800	Active TSS	Right Atrium	heart
9	chr1:171154400-171156600	Active TSS	Esophagus	oesophagus
10	chr1:171154400-171156600	Active TSS	Lung	lung
11	chr1:171154400-171156600	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr1:171154400-171156800	Active TSS	Right Ventricle	heart
13	chr1:171154600-171157200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:171154600-171157600	Weak transcription	Osteobl	bone
15	chr1:171154800-171157600	Weak transcription	Ovary	ovary
16	chr1:171155000-171157600	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:171155000-171158000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:171155600-171157400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:171155800-171157200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:171156000-171158400	Enhancers	Fetal Lung	lung
21	chr1:171156400-171156600	Enhancers	Fetal Intestine Large	intestine
22	chr1:171156400-171156600	Enhancers	Fetal Intestine Small	intestine
23	chr1:171156400-171156600	Enhancers	Small Intestine	intestine
24	chr1:171156400-171158000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:171156400-171165800	Weak transcription	Gastric	stomach

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