Variant report

Variant	rs13081855
Chromosome Location	chr3:99481539-99481540
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs13059876	0.82[TSI][hapmap]
rs13060898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13063594	1.00[JPT][hapmap]
rs13073356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074107	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13077478	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13079051	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13079056	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13079346	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13080329	0.86[MEX][hapmap]
rs13082013	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs13095226	0.82[TSI][hapmap]
rs13095282	1.00[JPT][hapmap]
rs13096116	0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs13097830	1.00[JPT][hapmap]
rs13100490	1.00[JPT][hapmap]
rs13100689	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17777354	0.82[TSI][hapmap]
rs17778253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34259523	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34265976	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34267913	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34510467	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34605311	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34795953	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886851	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35170022	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35431878	0.91[EUR][1000 genomes]
rs35445146	0.89[EUR][1000 genomes]
rs35468254	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35492383	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35522745	0.91[EUR][1000 genomes]
rs35640679	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35742383	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35804387	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62281858	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62281859	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62283460	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62283463	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62283465	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62283470	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62283488	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62283491	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283492	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62283493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62283494	0.82[AMR][1000 genomes]
rs62283495	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791889	0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs71313564	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7626245	0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs7636514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649862	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Age-related macular degeneration	23455636	GWAS catalog

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99462400-99495600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:99472400-99484000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:99472400-99484000	Weak transcription	NHLF	lung
4	chr3:99472400-99493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:99472400-99493000	Weak transcription	NHEK	skin
6	chr3:99472400-99493400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:99472600-99483800	Weak transcription	NH-A	brain
8	chr3:99474800-99486200	Weak transcription	NHDF-Ad	bronchial
9	chr3:99477600-99481600	Weak transcription	HUVEC	blood vessel
10	chr3:99479000-99482800	Enhancers	Adipose Nuclei	Adipose
11	chr3:99479200-99482200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:99479200-99482600	Weak transcription	Right Atrium	heart
13	chr3:99479200-99484000	Weak transcription	Aorta	Aorta
14	chr3:99479800-99482600	Weak transcription	Left Ventricle	heart
15	chr3:99480200-99482000	Enhancers	HSMMtube	muscle
16	chr3:99480200-99482000	Strong transcription	Osteobl	bone
17	chr3:99480600-99481600	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:99480600-99484000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:99480600-99484000	Weak transcription	Right Ventricle	heart
20	chr3:99481000-99482000	Genic enhancers	HSMM	muscle
21	chr3:99481200-99482000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:99481400-99481600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr3:99481400-99481600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:99481400-99481800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:99481400-99481800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:99481400-99481800	Enhancers	Psoas Muscle	Psoas
27	chr3:99481400-99482400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:99481400-99482800	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr3:99481400-99483000	Weak transcription	Fetal Heart	heart

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