Variant report

Variant	rs16883860
Chromosome Location	chr6:36002462-36002463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36002332..36004351-chr6:36041917..36043822,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112062	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10456082	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10456438	0.92[ASN][1000 genomes]
rs12204910	0.83[ASN][1000 genomes]
rs12206103	0.81[ASN][1000 genomes]
rs16883819	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884628	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884694	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs16884857	0.95[EUR][1000 genomes]
rs16884906	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967966	0.92[EUR][1000 genomes]
rs2237094	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.94[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804451	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804454	0.93[LWK][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.87[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]
rs56059109	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56133220	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	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56362075	0.91[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	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60100837	0.96[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	0.87[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	0.91[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	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6908622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914570	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921999	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6930333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407871	0.98[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73729685	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73729698	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73730437	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73730440	0.91[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745536	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745927	0.98[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	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7759175	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760405	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs7760578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761118	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[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	1.00[CEU][hapmap];0.86[CHB][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7771484	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7772088	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16883860	SLC26A8	cis	Thyroid	GTEx
rs16883860	SLC26A8	cis	multi-tissue	Pritchard
rs16883860	SLC26A8	cis	cerebellum	SCAN
rs16883860	SLC26A8	cis	Nerve Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35997400-36004000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:35997600-36002800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:35997600-36003200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:35997600-36004200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr6:35997600-36005400	Weak transcription	Aorta	Aorta
6	chr6:35997600-36005400	Weak transcription	Left Ventricle	heart
7	chr6:35997600-36008800	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr6:35997600-36010800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:35997600-36021800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:35998000-36003200	Weak transcription	Right Ventricle	heart
11	chr6:35998000-36003800	Enhancers	Colon Smooth Muscle	Colon
12	chr6:35998000-36004400	Enhancers	Fetal Lung	lung
13	chr6:35998000-36007400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr6:35998000-36019200	Weak transcription	HSMM	muscle
15	chr6:35998200-36002600	Enhancers	Liver	Liver
16	chr6:35998200-36006000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:35998200-36006600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:35998200-36018400	Weak transcription	NHLF	lung
19	chr6:35998200-36018600	Weak transcription	NHDF-Ad	bronchial
20	chr6:35998400-36003800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr6:35998600-36002600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:35998600-36007400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:35998800-36003800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:35998800-36003800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:35998800-36005600	Weak transcription	Fetal Brain Female	brain
26	chr6:35998800-36008800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:35999000-36003400	Enhancers	Stomach Mucosa	stomach
28	chr6:35999000-36027600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:35999200-36002800	Weak transcription	Pancreas	Pancrea
30	chr6:35999200-36004000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:35999400-36003200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:36000000-36004400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr6:36000200-36002800	Enhancers	Brain Angular Gyrus	brain
34	chr6:36000200-36003800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:36000200-36003800	Enhancers	Adipose Nuclei	Adipose
36	chr6:36000400-36003400	Enhancers	Brain Hippocampus Middle	brain
37	chr6:36000400-36005400	Weak transcription	HUVEC	blood vessel
38	chr6:36000600-36002800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr6:36000600-36003000	Weak transcription	Brain Substantia Nigra	brain
40	chr6:36000600-36005200	Weak transcription	Fetal Kidney	kidney
41	chr6:36000600-36005600	Weak transcription	Fetal Intestine Large	intestine
42	chr6:36000600-36005800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:36000600-36006000	Weak transcription	Dnd41	blood
44	chr6:36000600-36009800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:36000600-36020400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:36000600-36027400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:36000800-36009200	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:36001200-36003000	Genic enhancers	Fetal Intestine Small	intestine
49	chr6:36001200-36003200	Enhancers	Small Intestine	intestine
50	chr6:36001200-36003400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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