Variant report

Variant	rs56059109
Chromosome Location	chr6:36025307-36025308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36024238..36026339-chr6:36030286..36032254,2	K562	blood:
2	chr6:35995175..35997907-chr6:36024774..36027631,2	MCF-7	breast:
3	chr6:36017368..36019921-chr6:36022129..36025655,3	K562	blood:
4	chr6:36022269..36026633-chr6:36027844..36030184,4	K562	blood:

Variant related genes	Relation type
ENSG00000112062	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10456082	0.92[ASN][1000 genomes]
rs10456438	0.92[ASN][1000 genomes]
rs12204910	0.83[ASN][1000 genomes]
rs12206103	0.81[ASN][1000 genomes]
rs16883819	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884628	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884660	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884694	0.89[EUR][1000 genomes]
rs16884857	0.95[EUR][1000 genomes]
rs16884906	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884919	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967966	0.92[EUR][1000 genomes]
rs2237094	0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2237096	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730327	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730366	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761980	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804451	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804454	0.88[AFR][1000 genomes]
rs41271263	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55878630	0.83[ASN][1000 genomes]
rs56044978	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56133220	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156688	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56327416	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56362075	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56413204	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56715462	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58390233	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58583792	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58690654	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60100837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60342497	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60481532	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60909394	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61195139	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61212706	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61364424	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61763101	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457878	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6908622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910685	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914570	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6930333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932598	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936327	0.95[EUR][1000 genomes]
rs73407868	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407876	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73409842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73729685	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73729698	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73730437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73730440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73730459	0.92[EUR][1000 genomes]
rs7745082	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747846	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748078	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7752459	0.92[EUR][1000 genomes]
rs7759175	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760405	0.83[EUR][1000 genomes]
rs7760578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761118	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762483	0.95[EUR][1000 genomes]
rs7764494	0.92[EUR][1000 genomes]
rs7766032	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769981	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7770183	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7771484	0.95[EUR][1000 genomes]
rs7772088	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775290	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv528432	chr6:35958871-36035354	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56059109	SLC26A8	cis	Thyroid	GTEx
rs56059109	SLC26A8	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35999000-36027600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:36000600-36027400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:36003200-36027200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:36003800-36027600	Weak transcription	Colonic Mucosa	Colon
5	chr6:36006400-36039800	Weak transcription	Esophagus	oesophagus
6	chr6:36007400-36027200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:36008600-36027600	Weak transcription	Brain Substantia Nigra	brain
8	chr6:36017800-36029400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:36018200-36027200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:36018200-36050000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:36018600-36026200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:36018600-36027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:36018800-36027400	Weak transcription	NHEK	skin
14	chr6:36019000-36027600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:36019400-36026400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:36019400-36026400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:36019400-36026400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:36019400-36027000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:36019400-36027200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:36019400-36027200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:36019400-36032600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:36019600-36027000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:36019600-36027400	Weak transcription	Pancreas	Pancrea
24	chr6:36019600-36027400	Weak transcription	Right Ventricle	heart
25	chr6:36019600-36027600	Weak transcription	Gastric	stomach
26	chr6:36019800-36031600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr6:36020000-36027200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:36020000-36027200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:36020000-36027400	Weak transcription	Spleen	Spleen
30	chr6:36020000-36027600	Weak transcription	A549	lung
31	chr6:36020000-36033800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr6:36020200-36026600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr6:36020200-36027600	Weak transcription	NHLF	lung
34	chr6:36020400-36027000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:36020400-36032600	Weak transcription	Right Atrium	heart
36	chr6:36020400-36033000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:36020400-36047400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:36020600-36025400	Strong transcription	Hela-S3	cervix
39	chr6:36020600-36027200	Weak transcription	Adipose Nuclei	Adipose
40	chr6:36020800-36029200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:36021200-36027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:36021600-36027200	Weak transcription	HMEC	breast
43	chr6:36021600-36033200	Weak transcription	Fetal Brain Male	brain
44	chr6:36021800-36027000	Weak transcription	Placenta	Placenta
45	chr6:36021800-36027200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:36022000-36027000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:36022000-36027200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:36022000-36027200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:36022000-36032200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:36022000-36088800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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