Variant report

Variant	rs983889
Chromosome Location	chr5:15555486-15555487
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10037317	0.83[EUR][1000 genomes]
rs13184823	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366651	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366653	0.81[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1429037	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1429039	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1429040	0.81[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1429041	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1835130	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1835131	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1835132	0.85[EUR][1000 genomes]
rs1835133	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1978633	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2402166	0.88[EUR][1000 genomes]
rs2402167	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4702084	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4702086	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6420022	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6420023	0.85[ASN][1000 genomes]
rs6554887	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554888	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6895002	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7733607	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7734082	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312893	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9312894	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs969351	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs972182	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15512200-15571200	Weak transcription	HUVEC	blood vessel
2	chr5:15524000-15558600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:15536400-15561400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:15541000-15558600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:15544600-15563400	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:15545200-15557600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:15547800-15557600	Weak transcription	Right Ventricle	heart
8	chr5:15548200-15557800	Weak transcription	Left Ventricle	heart
9	chr5:15548600-15557600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:15550600-15556400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:15551000-15561600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:15551200-15559400	Weak transcription	Fetal Brain Male	brain
13	chr5:15551200-15566200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:15551400-15558400	Weak transcription	Aorta	Aorta
15	chr5:15551400-15566800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:15551600-15561400	Weak transcription	Fetal Lung	lung
17	chr5:15551600-15561600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:15551600-15561800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:15551800-15557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:15552800-15556400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:15553400-15557200	Weak transcription	Fetal Stomach	stomach
22	chr5:15553800-15555600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr5:15553800-15555800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr5:15554000-15555800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr5:15554000-15555800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:15554200-15555800	Enhancers	Fetal Muscle Leg	muscle
27	chr5:15554600-15555600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr5:15554600-15555800	Enhancers	HSMM	muscle
29	chr5:15554800-15555600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr5:15555000-15555800	Enhancers	HSMMtube	muscle
31	chr5:15555000-15557600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:15555000-15557600	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:15555200-15555600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:15555200-15555600	Enhancers	Dnd41	blood
35	chr5:15555200-15555800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr5:15555200-15556000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:15555200-15557600	Weak transcription	Fetal Heart	heart
38	chr5:15555400-15555600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr5:15555400-15557800	Weak transcription	H9 Cell Line	embryonic stem cell

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