Variant report

Variant	rs6493086
Chromosome Location	chr15:43655394-43655395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43646115..43650025-chr15:43654953..43659195,5	K562	blood:

Extended variants
information (count: 140 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1058298	0.82[EUR][1000 genomes]
rs1095386	0.97[ASN][1000 genomes]
rs11070399	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123947	1.00[ASN][1000 genomes]
rs1133395	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637572	0.81[EUR][1000 genomes]
rs11858152	0.97[ASN][1000 genomes]
rs12101673	0.98[ASN][1000 genomes]
rs12102205	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148735	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12323999	0.92[ASN][1000 genomes]
rs12324572	1.00[ASN][1000 genomes]
rs12324584	0.92[ASN][1000 genomes]
rs12905772	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549523	1.00[ASN][1000 genomes]
rs1549525	1.00[ASN][1000 genomes]
rs16957627	1.00[ASN][1000 genomes]
rs16957630	1.00[ASN][1000 genomes]
rs16957632	1.00[ASN][1000 genomes]
rs1837959	0.87[ASN][1000 genomes]
rs1837960	0.87[ASN][1000 genomes]
rs2012467	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242068	0.84[ASN][1000 genomes]
rs2243434	0.88[ASN][1000 genomes]
rs2244746	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2244981	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2249952	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2253807	0.83[AMR][1000 genomes]
rs2264050	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2278856	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278857	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278859	1.00[ASN][1000 genomes]
rs2278860	1.00[ASN][1000 genomes]
rs2412778	1.00[ASN][1000 genomes]
rs2412779	1.00[ASN][1000 genomes]
rs2412780	1.00[ASN][1000 genomes]
rs2412781	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412782	0.90[ASN][1000 genomes]
rs2439845	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2439846	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2444036	0.89[ASN][1000 genomes]
rs2444037	0.84[EUR][1000 genomes]
rs2444251	0.82[EUR][1000 genomes]
rs2467733	0.89[ASN][1000 genomes]
rs2467737	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2467738	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2467741	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2467742	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2467745	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2584700	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2584701	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2584702	0.92[ASN][1000 genomes]
rs2584703	0.87[ASN][1000 genomes]
rs2602141	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28415933	1.00[ASN][1000 genomes]
rs28461955	1.00[ASN][1000 genomes]
rs28649346	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28653441	0.95[ASN][1000 genomes]
rs28702649	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729853	0.95[ASN][1000 genomes]
rs2899082	1.00[ASN][1000 genomes]
rs3213990	0.96[ASN][1000 genomes]
rs3213991	0.97[ASN][1000 genomes]
rs3742969	0.99[ASN][1000 genomes]
rs3742971	0.99[ASN][1000 genomes]
rs3809482	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075674	1.00[ASN][1000 genomes]
rs4296223	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4401024	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547312	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583210	1.00[ASN][1000 genomes]
rs478028	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478104	0.90[ASN][1000 genomes]
rs484029	0.99[ASN][1000 genomes]
rs484846	0.92[ASN][1000 genomes]
rs485148	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs488756	0.97[ASN][1000 genomes]
rs491800	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs498837	0.92[ASN][1000 genomes]
rs499035	0.92[ASN][1000 genomes]
rs507178	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509306	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs510108	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511673	0.99[ASN][1000 genomes]
rs512628	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518288	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs528517	0.97[ASN][1000 genomes]
rs536313	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs538238	0.86[EUR][1000 genomes]
rs540031	0.97[ASN][1000 genomes]
rs542898	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs548704	0.81[EUR][1000 genomes]
rs552701	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs560191	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs573615	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576557	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493081	0.99[ASN][1000 genomes]
rs6493082	1.00[ASN][1000 genomes]
rs6493083	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493084	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493085	1.00[ASN][1000 genomes]
rs6493087	0.82[ASN][1000 genomes]
rs6493088	0.97[ASN][1000 genomes]
rs689693	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689767	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690012	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690276	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs690367	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690446	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690472	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs690512	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs693510	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs694725	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7163245	0.95[ASN][1000 genomes]
rs7165471	1.00[ASN][1000 genomes]
rs7166812	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167882	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168940	0.97[ASN][1000 genomes]
rs7170152	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7170489	1.00[ASN][1000 genomes]
rs7172374	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175434	0.99[ASN][1000 genomes]
rs7176849	0.92[ASN][1000 genomes]
rs8033714	0.96[ASN][1000 genomes]
rs8039638	0.97[ASN][1000 genomes]
rs8041132	1.00[ASN][1000 genomes]
rs8042688	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs825739	0.87[ASN][1000 genomes]
rs825740	0.87[ASN][1000 genomes]
rs884704	0.90[ASN][1000 genomes]
rs933941	1.00[ASN][1000 genomes]
rs956391	0.98[ASN][1000 genomes]
rs9920879	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999026	0.90[ASN][1000 genomes]
rs999047	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS 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	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6493086	TGM5	cis	multi-tissue	Pritchard
rs6493086	STRCP1	cis	Esophagus Muscularis	GTEx
rs6493086	ADAL	cis	Nerve Tibial	GTEx
rs6493086	AC011330.5	cis	Thyroid	GTEx
rs6493086	ZSCAN29	cis	Thyroid	GTEx
rs6493086	TGM7	cis	Esophagus Mucosa	GTEx
rs6493086	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43646800-43656200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:43649200-43655400	ZNF genes & repeats	Fetal Intestine Large	intestine
3	chr15:43649200-43658600	ZNF genes & repeats	Liver	Liver
4	chr15:43649800-43660000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr15:43649800-43660200	ZNF genes & repeats	Fetal Muscle Leg	muscle
6	chr15:43650200-43656800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
7	chr15:43650200-43657000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr15:43650200-43657400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:43650200-43657600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
10	chr15:43650200-43657800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:43650200-43657800	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr15:43650200-43658600	ZNF genes & repeats	GM12878-XiMat	blood
13	chr15:43650200-43659800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:43650200-43660400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr15:43650200-43661600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:43650400-43656200	ZNF genes & repeats	NH-A	brain
17	chr15:43650400-43656600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr15:43650400-43657000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:43650400-43657600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:43650400-43658800	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr15:43650600-43656600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr15:43650600-43661400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:43650800-43656400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:43650800-43656400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
25	chr15:43650800-43656400	ZNF genes & repeats	HMEC	breast
26	chr15:43650800-43656400	ZNF genes & repeats	Osteobl	bone
27	chr15:43650800-43656600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:43650800-43656800	ZNF genes & repeats	NHLF	lung
29	chr15:43650800-43657600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr15:43650800-43659800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:43650800-43660200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:43651000-43656000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
33	chr15:43651000-43656600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:43651000-43656600	ZNF genes & repeats	Fetal Kidney	kidney
35	chr15:43651000-43656800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
36	chr15:43651000-43659800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr15:43651000-43660000	ZNF genes & repeats	Fetal Lung	lung
38	chr15:43651000-43660200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr15:43651000-43660400	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr15:43651200-43656600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr15:43651600-43655400	ZNF genes & repeats	Thymus	Thymus
42	chr15:43651600-43656000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
43	chr15:43651600-43656600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
44	chr15:43651600-43656800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:43651800-43656600	ZNF genes & repeats	HUVEC	blood vessel
46	chr15:43652800-43655600	ZNF genes & repeats	Brain Germinal Matrix	brain
47	chr15:43652800-43655800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:43652800-43656000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
49	chr15:43652800-43656000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
50	chr15:43652800-43656000	ZNF genes & repeats	Fetal Brain Female	brain

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