Variant report

Variant	rs28539215
Chromosome Location	chr5:61848684-61848685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10054305	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10058044	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10060589	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10065749	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10069745	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10071568	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10072795	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1301063	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13174978	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149540	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs149599	0.80[ASN][1000 genomes]
rs152184	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs152191	0.85[ASN][1000 genomes]
rs152199	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152202	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152203	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152208	0.86[ASN][1000 genomes]
rs152209	0.85[ASN][1000 genomes]
rs152215	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1541677	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1562244	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs166005	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs173523	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247233	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247240	0.85[ASN][1000 genomes]
rs247244	0.85[ASN][1000 genomes]
rs247248	0.85[ASN][1000 genomes]
rs26631	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs26632	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs26637	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26641	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26644	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27693	0.85[ASN][1000 genomes]
rs28581963	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615140	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34562047	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776638	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40110	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6449601	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6449602	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6881888	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6888641	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7717128	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7722692	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7729526	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7737525	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs784921	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs918606	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv881729	chr5:61719506-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv881730	chr5:61750667-61883581	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1020713	chr5:61786309-61921150	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv537770	chr5:61786309-61921150	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv881731	chr5:61794164-61941043	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv881732	chr5:61811970-62063366	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv881733	chr5:61828147-61877628	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv881734	chr5:61828147-61921815	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv881735	chr5:61831283-61877628	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv881736	chr5:61833440-61877628	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61739200-61862800	Weak transcription	Brain Substantia Nigra	brain
2	chr5:61748000-61862800	Weak transcription	Right Ventricle	heart
3	chr5:61758800-61890000	Weak transcription	Small Intestine	intestine
4	chr5:61764000-61858200	Weak transcription	Placenta	Placenta
5	chr5:61764200-61895800	Weak transcription	Pancreas	Pancrea
6	chr5:61766200-61849800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:61771200-61864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:61771400-61863000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:61772200-61850800	Weak transcription	HSMMtube	muscle
10	chr5:61781600-61867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:61787400-61866800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:61793600-61905000	Weak transcription	NHEK	skin
13	chr5:61795200-61850600	Weak transcription	Fetal Intestine Small	intestine
14	chr5:61796600-61866600	Weak transcription	Osteobl	bone
15	chr5:61796800-61899000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:61797000-61861200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:61802600-61889000	Weak transcription	NH-A	brain
18	chr5:61803000-61904400	Weak transcription	Fetal Kidney	kidney
19	chr5:61803200-61875000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:61803400-61855000	Weak transcription	HSMM	muscle
21	chr5:61803400-61863600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:61804400-61865200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:61806800-61863400	Weak transcription	Lung	lung
24	chr5:61812200-61865200	Weak transcription	HUVEC	blood vessel
25	chr5:61815000-61861400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:61815200-61890600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:61816000-61857800	Weak transcription	Fetal Stomach	stomach
28	chr5:61816200-61862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:61819200-61860400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:61819800-61861600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:61821400-61863400	Weak transcription	Aorta	Aorta
32	chr5:61822600-61849000	Weak transcription	A549	lung
33	chr5:61823200-61856000	Weak transcription	Fetal Heart	heart
34	chr5:61827200-61850200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:61827200-61856000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:61827200-61858200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:61827200-61861200	Weak transcription	Liver	Liver
38	chr5:61827200-61883600	Weak transcription	HepG2	liver
39	chr5:61827400-61862800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:61827400-61899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:61827600-61856000	Weak transcription	Fetal Thymus	thymus
42	chr5:61828200-61850800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:61828200-61854800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:61828200-61855800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:61828200-61861600	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:61828200-61862800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr5:61828200-61864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:61828200-61886800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:61828600-61855000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:61828600-61858000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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