Variant report

Variant	rs399271
Chromosome Location	chr5:9483472-9483473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs166535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs169163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1700580	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs171992	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs198686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs268469	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268470	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs268471	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs268472	0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs268473	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268474	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268476	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs268493	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs268494	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs268495	0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs268496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268497	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268498	0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs268499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs268500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs268501	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs268502	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs268503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs268504	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs268508	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs268509	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs268516	0.90[CHB][hapmap]
rs268517	0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs268518	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268519	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268520	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs268522	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs377947	0.87[ASN][1000 genomes]
rs3798036	0.86[CHB][hapmap]
rs388157	0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs389520	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs389537	0.86[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs391353	0.84[ASN][1000 genomes]
rs418373	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs418446	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs421548	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs422556	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs435128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs438343	0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs438506	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs442173	0.90[CHB][hapmap]
rs444808	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs446904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs524976	0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs570834	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs645696	0.81[CHB][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs813717	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9478600-9511000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:9478600-9515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:9478800-9483600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:9478800-9504000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:9479600-9508200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:9480400-9483600	Weak transcription	Osteobl	bone
7	chr5:9480800-9490800	Weak transcription	Left Ventricle	heart
8	chr5:9482400-9485200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:9482400-9486200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:9482600-9483800	Enhancers	HMEC	breast
11	chr5:9482600-9484000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:9482600-9484000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:9482600-9484200	Enhancers	NH-A	brain
14	chr5:9482600-9484400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:9482600-9485000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr5:9482800-9484200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:9482800-9484400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:9482800-9484400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:9482800-9486200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:9483000-9483600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:9483000-9483800	Enhancers	NHEK	skin
22	chr5:9483000-9484000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:9483000-9484400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr5:9483000-9484400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr5:9483000-9484600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:9483000-9484600	Enhancers	NHLF	lung
27	chr5:9483000-9484800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:9483000-9486000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:9483000-9490800	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:9483200-9483800	Enhancers	Fetal Heart	heart
31	chr5:9483200-9484000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:9483200-9484000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:9483200-9484000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:9483200-9484200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:9483200-9484400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:9483200-9484600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr5:9483200-9484800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:9483400-9483600	Flanking Active TSS	NHDF-Ad	bronchial
39	chr5:9483400-9483800	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr5:9483400-9483800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr5:9483400-9483800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:9483400-9484600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr5:9483400-9484600	Enhancers	Fetal Lung	lung

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