Variant report

Variant	rs12659413
Chromosome Location	chr5:15718184-15718185
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10044254	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs10051629	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs10066645	0.85[AMR][1000 genomes]
rs10520821	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11950539	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11951416	0.84[MKK][hapmap]
rs12515897	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519807	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12653727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13172068	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358928	0.82[CEU][hapmap]
rs1394654	0.84[AMR][1000 genomes]
rs1394656	0.83[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs1394657	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs16867615	0.89[YRI][hapmap]
rs16867617	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs2937073	0.88[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes]
rs2937075	0.86[YRI][hapmap]
rs2938832	0.83[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes]
rs2964268	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs4146556	0.82[YRI][hapmap]
rs4235553	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4235554	0.83[LWK][hapmap];0.93[YRI][hapmap]
rs4235556	0.80[YRI][hapmap]
rs4273602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4293917	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4461631	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4475263	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4482903	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4601044	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4701641	0.80[AMR][1000 genomes]
rs4702093	0.82[EUR][1000 genomes]
rs4702100	0.84[GIH][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.86[AMR][1000 genomes]
rs6554899	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554900	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554901	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554902	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884087	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6885069	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72732056	0.89[ASN][1000 genomes]
rs7704590	0.83[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7707563	0.84[GIH][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs7720498	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7725413	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7732283	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7736983	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv597263	chr5:15672137-15720478	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv461983	chr5:15674635-15720106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv597264	chr5:15674635-15720106	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv2757107	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2759327	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv432718	chr5:15688927-15723346	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv2756126	chr5:15700541-15720478	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv2763894	chr5:15714022-15863332	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	esv2760924	chr5:15716127-15730060	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15701400-15718200	Weak transcription	Fetal Lung	lung
2	chr5:15705600-15718600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:15715200-15720600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:15715600-15718200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:15715600-15720400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:15715600-15720600	Enhancers	Fetal Heart	heart
7	chr5:15715800-15718200	Enhancers	NHDF-Ad	bronchial
8	chr5:15716000-15718400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:15716200-15718800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:15716600-15718400	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:15716600-15718600	Weak transcription	Ovary	ovary
12	chr5:15716600-15718800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:15716600-15719000	Weak transcription	Brain Anterior Caudate	brain
14	chr5:15716600-15721000	Enhancers	HUVEC	blood vessel
15	chr5:15716800-15719000	Weak transcription	Brain Substantia Nigra	brain
16	chr5:15716800-15719800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:15717000-15718800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:15717200-15718800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:15717400-15718400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:15717400-15719000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:15717400-15719400	Weak transcription	Right Ventricle	heart
22	chr5:15717400-15720000	Weak transcription	Left Ventricle	heart
23	chr5:15717400-15721400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:15717600-15718200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:15717600-15718400	Weak transcription	Osteobl	bone
26	chr5:15717600-15718600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:15717600-15718600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:15717600-15718600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:15717600-15718600	Weak transcription	Aorta	Aorta
30	chr5:15717600-15718800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:15717600-15719000	Weak transcription	Fetal Stomach	stomach
32	chr5:15717600-15719000	Weak transcription	Right Atrium	heart
33	chr5:15717600-15719800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:15717600-15720000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:15717600-15721400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:15717800-15718200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:15717800-15718600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:15717800-15719600	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:15717800-15719800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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