Variant report

Variant	rs62023809
Chromosome Location	chr15:99867079-99867080
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12148825	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510059	0.87[EUR][1000 genomes]
rs2136628	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28651946	0.90[EUR][1000 genomes]
rs28729666	0.89[EUR][1000 genomes]
rs4640164	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58762669	0.89[EUR][1000 genomes]
rs59136665	0.90[EUR][1000 genomes]
rs59855164	0.87[EUR][1000 genomes]
rs62023803	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62023804	0.91[ASN][1000 genomes]
rs62023806	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023807	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023810	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023811	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023845	0.91[ASN][1000 genomes]
rs62023846	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62023847	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62023852	0.90[EUR][1000 genomes]
rs62023854	0.90[EUR][1000 genomes]
rs62023857	0.89[EUR][1000 genomes]
rs62023858	0.89[EUR][1000 genomes]
rs62025360	0.87[EUR][1000 genomes]
rs62025361	0.87[EUR][1000 genomes]
rs62025363	0.87[EUR][1000 genomes]
rs62025364	0.86[EUR][1000 genomes]
rs62025365	0.87[EUR][1000 genomes]
rs62025366	0.81[EUR][1000 genomes]
rs62025367	0.82[EUR][1000 genomes]
rs62025695	0.81[ASN][1000 genomes]
rs6422002	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181876	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181973	0.83[EUR][1000 genomes]
rs8032790	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8033188	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041236	0.91[EUR][1000 genomes]
rs978703	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh 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	45 gene(s)	inside rSNPs	diseases
6	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS 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	30 gene(s)	inside rSNPs	diseases
9	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
10	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers 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	47 gene(s)	inside rSNPs	diseases
17	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62023809	SYNM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
2	chr15:99847400-99877200	Weak transcription	Ovary	ovary
3	chr15:99853000-99876000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:99853200-99875400	Weak transcription	Fetal Thymus	thymus
5	chr15:99853600-99875800	Weak transcription	Fetal Intestine Large	intestine
6	chr15:99854400-99876000	Weak transcription	Dnd41	blood
7	chr15:99858600-99876600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:99859400-99906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:99860600-99867200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:99860600-99867200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:99860600-99869200	Enhancers	HepG2	liver
12	chr15:99861800-99876600	Weak transcription	Primary T cells from cord blood	blood
13	chr15:99863200-99881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:99863200-99899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:99864400-99902200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:99864600-99877200	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:99864800-99867200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr15:99864800-99867200	Enhancers	NHEK	skin
19	chr15:99864800-99881400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:99864800-99884200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:99865200-99867200	Enhancers	HMEC	breast
22	chr15:99865200-99870800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:99865200-99875800	Weak transcription	Adipose Nuclei	Adipose
24	chr15:99865200-99880600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:99865400-99870800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:99866000-99867200	Flanking Active TSS	A549	lung
27	chr15:99866200-99868600	Enhancers	Liver	Liver
28	chr15:99866200-99869600	Weak transcription	GM12878-XiMat	blood
29	chr15:99866800-99868400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:99866800-99871600	Weak transcription	HSMMtube	muscle
31	chr15:99866800-99875600	Weak transcription	Left Ventricle	heart
32	chr15:99866800-99875800	Weak transcription	Pancreas	Pancrea
33	chr15:99866800-99877400	Weak transcription	Right Ventricle	heart
34	chr15:99866800-99877800	Weak transcription	Psoas Muscle	Psoas
35	chr15:99866800-99881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:99866800-99882400	Weak transcription	Gastric	stomach
37	chr15:99867000-99871200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:99867000-99880600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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