Variant report

Variant	rs12487817
Chromosome Location	chr3:50562566-50562567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50561864..50565057-chr3:50565315..50568645,4	K562	blood:
2	chr3:50553722..50555461-chr3:50562201..50564334,2	K562	blood:
3	chr3:50560226..50564542-chr3:50564835..50568102,5	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1077215	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap]
rs1107312	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486143	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486717	0.82[AMR][1000 genomes]
rs12489607	0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs12491440	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs12491812	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492093	0.83[AMR][1000 genomes]
rs12492540	0.83[AMR][1000 genomes]
rs12492982	0.83[AMR][1000 genomes]
rs12494094	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494326	0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17050991	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17050995	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17051000	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051043	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs17051045	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs17051403	0.88[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs1872184	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1894459	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2035484	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs2076927	0.82[AMR][1000 genomes]
rs2170840	0.89[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2227292	0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2227293	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239750	0.90[ASN][1000 genomes]
rs2239751	0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239752	0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239753	0.83[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2285090	0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3749265	0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3752449	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3792323	0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3806706	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4476497	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4640555	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4688705	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes]
rs4688707	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688709	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4688710	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688713	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688715	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4688716	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56170012	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56856095	0.82[AMR][1000 genomes]
rs57910827	0.83[AMR][1000 genomes]
rs58427389	0.82[ASN][1000 genomes]
rs59036236	0.82[AMR][1000 genomes]
rs60552073	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60877431	0.83[AMR][1000 genomes]
rs61193866	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61316441	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61574029	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61613532	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616689	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6446208	0.87[AMR][1000 genomes]
rs650655	0.87[AMR][1000 genomes]
rs6766638	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771348	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6783922	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6794155	0.86[AMR][1000 genomes]
rs728902	0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs72938758	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942785	0.83[AMR][1000 genomes]
rs72942794	0.83[AMR][1000 genomes]
rs73835531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743753	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs745356	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs762889	0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs808148	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs876103	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes]
rs876104	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs876105	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes]
rs9814874	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs9868889	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9879397	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][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	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50553800-50563000	Weak transcription	K562	blood
2	chr3:50554600-50563200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:50556000-50563000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:50558600-50563000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:50558800-50570600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:50559200-50563400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:50559600-50564600	Enhancers	Fetal Intestine Small	intestine
8	chr3:50559800-50563000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:50559800-50564800	Enhancers	Fetal Intestine Large	intestine
10	chr3:50560600-50563600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:50560600-50564000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:50561200-50562600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:50561200-50562600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:50561400-50563000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:50561400-50567200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:50562000-50563600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:50562000-50564400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:50562200-50565000	Enhancers	Brain Germinal Matrix	brain
19	chr3:50562400-50562600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:50562400-50562800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:50562400-50563600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr3:50562400-50564000	Enhancers	H1 Cell Line	embryonic stem cell

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