Variant report

Variant	rs59974698
Chromosome Location	chr15:42558280-42558281
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12437600	0.92[ASN][1000 genomes]
rs12438369	0.84[ASN][1000 genomes]
rs12438509	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440087	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441016	0.94[ASN][1000 genomes]
rs12441642	0.84[ASN][1000 genomes]
rs1659213	0.86[AMR][1000 genomes]
rs1659218	0.89[AMR][1000 genomes]
rs1659219	0.89[AMR][1000 genomes]
rs1659221	0.89[AMR][1000 genomes]
rs1659222	0.89[AMR][1000 genomes]
rs1678984	0.89[AMR][1000 genomes]
rs1678992	0.89[AMR][1000 genomes]
rs1678993	0.82[AMR][1000 genomes]
rs16972770	0.81[AMR][1000 genomes]
rs16972776	0.86[AMR][1000 genomes]
rs16972887	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973008	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973045	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16973060	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2138831	0.86[ASN][1000 genomes]
rs2407707	0.89[ASN][1000 genomes]
rs2412688	1.00[ASN][1000 genomes]
rs28364388	0.84[ASN][1000 genomes]
rs2918460	0.89[AMR][1000 genomes]
rs3736099	0.89[ASN][1000 genomes]
rs3743005	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3743007	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3743008	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3825785	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4506867	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4923932	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4923945	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924627	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4924630	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924631	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4924644	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924672	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924673	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4924674	0.84[ASN][1000 genomes]
rs55882551	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56257215	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56670003	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56702977	0.84[ASN][1000 genomes]
rs56987883	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57134130	0.84[ASN][1000 genomes]
rs57393446	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57933952	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57973092	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57976413	1.00[ASN][1000 genomes]
rs58292736	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58313689	0.92[ASN][1000 genomes]
rs58712370	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59094161	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59132828	0.95[ASN][1000 genomes]
rs59138723	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59320762	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59893734	0.89[ASN][1000 genomes]
rs60443443	0.89[ASN][1000 genomes]
rs60506946	0.81[AMR][1000 genomes]
rs60634548	1.00[ASN][1000 genomes]
rs61069354	1.00[ASN][1000 genomes]
rs61133768	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6493033	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179203	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7180279	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7181979	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73398938	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73400993	0.89[ASN][1000 genomes]
rs73402707	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73403365	1.00[ASN][1000 genomes]
rs73403546	0.81[AMR][1000 genomes]
rs73403548	0.83[AMR][1000 genomes]
rs73403550	0.81[AMR][1000 genomes]
rs73407403	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73407407	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73407488	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409577	0.97[ASN][1000 genomes]
rs8025601	0.95[ASN][1000 genomes]
rs8027016	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8041951	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42519400-42562800	Weak transcription	Fetal Heart	heart
3	chr15:42520200-42561000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:42542800-42561600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:42543400-42559000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:42543400-42561200	Strong transcription	Liver	Liver
7	chr15:42543600-42561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:42543800-42560200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr15:42543800-42560800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr15:42543800-42561600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:42544000-42560600	Strong transcription	Adipose Nuclei	Adipose
12	chr15:42544000-42560800	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:42544200-42561000	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr15:42544200-42561200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr15:42544200-42561200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:42544200-42561800	Strong transcription	Osteobl	bone
17	chr15:42544400-42561200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:42544400-42561200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:42544600-42560600	Strong transcription	Placenta	Placenta
20	chr15:42544600-42560800	Strong transcription	Fetal Thymus	thymus
21	chr15:42544600-42561600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:42544800-42559800	Strong transcription	Fetal Kidney	kidney
23	chr15:42544800-42560800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:42545000-42561400	Strong transcription	HSMM	muscle
25	chr15:42545200-42560600	Strong transcription	HepG2	liver
26	chr15:42545200-42560800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:42545400-42560400	Strong transcription	Primary T cells from cord blood	blood
28	chr15:42545400-42560400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr15:42545400-42560800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:42545600-42559400	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:42545600-42563400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:42545800-42558600	Strong transcription	Primary B cells from cord blood	blood
33	chr15:42545800-42560400	Strong transcription	Fetal Intestine Large	intestine
34	chr15:42545800-42561400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:42546000-42560800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:42546000-42564600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:42546200-42558400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:42546200-42564600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:42546400-42559200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:42546400-42561000	Strong transcription	Dnd41	blood
41	chr15:42546600-42560800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:42546600-42561600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:42546800-42559400	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:42546800-42560800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:42547000-42564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:42547400-42559200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:42547600-42561200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:42547600-42563400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:42547800-42558600	Strong transcription	Brain Germinal Matrix	brain
50	chr15:42548000-42560600	Strong transcription	H1 Cell Line	embryonic stem cell

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