Variant report

Variant	rs3761980
Chromosome Location	chr6:35993906-35993907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:35993299-35994001	K562	blood:	n/a	n/a
2	PBX3	chr6:35993635-35994200	SK-N-SH	brain:	n/a	n/a
3	FOS	chr6:35993354-35994202	HUVEC	blood vessel:	n/a	chr6:35993572-35993583
4	TEAD4	chr6:35993118-35994061	K562	blood:	n/a	n/a
5	GATA3	chr6:35993233-35994152	SK-N-SH	brain:	n/a	chr6:35993525-35993532 chr6:35993518-35993539 chr6:35993520-35993536 chr6:35993525-35993532 chr6:35993525-35993532
6	TCF12	chr6:35993274-35994257	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:35993886-35994233	K562	blood:	n/a	n/a
8	JUND	chr6:35993797-35994114	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr6:35993793-35994127	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:35993690-35994103	SK-N-SH	brain:	n/a	n/a
11	GATA2	chr6:35993277-35994207	HUVEC	blood vessel:	n/a	chr6:35993525-35993532 chr6:35993518-35993539 chr6:35993520-35993536 chr6:35993525-35993532 chr6:35993525-35993532
12	HEY1	chr6:35993878-35994237	K562	blood:	n/a	n/a
13	POLR2A	chr6:35993259-35994134	HUVEC	blood vessel:	n/a	n/a
14	GATA3	chr6:35993280-35994200	SK-N-SH	brain:	n/a	chr6:35993525-35993532 chr6:35993518-35993539 chr6:35993520-35993536 chr6:35993525-35993532 chr6:35993525-35993532
15	TCF12	chr6:35993580-35994170	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:35993372..35995474-chr6:36048544..36050662,2	K562	blood:
2	chr6:35992919..35998420-chr6:36043527..36047632,6	K562	blood:
3	chr6:35992707..35998254-chr6:36162958..36166458,7	K562	blood:
4	chr6:35887479..35890120-chr6:35993309..35995768,2	K562	blood:
5	chr6:35992836..35995217-chr6:36030418..36034418,3	K562	blood:
6	chr6:35991723..36001946-chr6:36059635..36067870,13	K562	blood:
7	chr6:35993265..35998448-chr6:36161633..36166981,11	K562	blood:
8	chr6:35993804..35995388-chr6:36064121..36065946,2	MCF-7	breast:

Variant related genes	Relation type
SLC26A8	TF binding region
MAPK14	TF binding region
ENSG00000096063	Chromatin interaction
ENSG00000096070	Chromatin interaction
ENSG00000246982	Chromatin interaction
ENSG00000112062	Chromatin interaction
ENSG00000237719	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];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs10456438	0.95[ASN][1000 genomes]
rs12204910	0.86[ASN][1000 genomes]
rs12206103	0.83[ASN][1000 genomes]
rs16883819	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16883860	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]
rs16883989	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16884628	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16884660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16884919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1967966	0.92[EUR][1000 genomes]
rs2237094	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2237096	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3730327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3730366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804451	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804454	0.86[LWK][hapmap]
rs41271263	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55878630	0.86[ASN][1000 genomes]
rs56044978	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56059109	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56133220	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56156688	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56327416	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56362075	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56413204	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56715462	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58390233	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58583792	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58690654	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60100837	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60342497	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60481532	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60909394	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61195139	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61212706	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61364424	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61763101	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457878	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6908622	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910685	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914570	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921999	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6932598	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6934216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936327	0.95[EUR][1000 genomes]
rs73407868	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73407870	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73407871	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73407876	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73409842	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73729685	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73729698	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73730437	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73730440	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73730459	0.92[EUR][1000 genomes]
rs7745082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745536	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7745927	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7747846	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7748078	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7752459	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7759175	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760405	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs7760578	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761118	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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];0.97[ASN][1000 genomes]
rs7769981	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7770183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7771484	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7772088	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7775290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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
rs3761980	SLC26A8	cis	Thyroid	GTEx
rs3761980	SLC26A8	cis	cerebellum	SCAN
rs3761980	SLC26A8	cis	multi-tissue	Pritchard
rs3761980	SLC26A8	cis	Nerve Tibial	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35992000-35994800	Enhancers	NHLF	lung
2	chr6:35992200-35994200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:35992400-35994400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:35992400-35995000	Weak transcription	Colonic Mucosa	Colon
5	chr6:35992400-35995400	Weak transcription	Esophagus	oesophagus
6	chr6:35992400-35995400	Weak transcription	Lung	lung
7	chr6:35992400-35995400	Weak transcription	Right Atrium	heart
8	chr6:35992600-35995000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:35992600-35995000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:35992600-35995000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:35992600-35995000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:35992600-35995000	Weak transcription	HMEC	breast
13	chr6:35992600-35995000	Enhancers	HUVEC	blood vessel
14	chr6:35992600-35995400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:35992600-35995400	Weak transcription	Brain Angular Gyrus	brain
16	chr6:35992600-35995400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:35992600-35995400	Weak transcription	Gastric	stomach
18	chr6:35992600-35995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:35992800-35995000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:35992800-35995000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:35992800-35995000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:35992800-35995000	Weak transcription	Brain Anterior Caudate	brain
23	chr6:35992800-35995000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:35992800-35995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:35992800-35995000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:35992800-35995000	Weak transcription	Thymus	Thymus
27	chr6:35992800-35995000	Weak transcription	NHEK	skin
28	chr6:35992800-35995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:35992800-35995600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:35993000-35994400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr6:35993000-35994600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:35993000-35994800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr6:35993000-35995000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:35993000-35995000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:35993000-35995000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:35993000-35995000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:35993000-35995000	Weak transcription	Fetal Thymus	thymus
38	chr6:35993000-35995200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:35993000-35995400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:35993000-35995400	Weak transcription	Spleen	Spleen
41	chr6:35993200-35994200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:35993200-35994200	Enhancers	Fetal Heart	heart
43	chr6:35993200-35994200	Flanking Active TSS	K562	blood
44	chr6:35993200-35995000	Enhancers	Osteobl	bone
45	chr6:35993400-35994000	Enhancers	NHDF-Ad	bronchial
46	chr6:35993400-35994400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr6:35993400-35994800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:35993400-35995000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr6:35993400-35995000	Enhancers	HepG2	liver
50	chr6:35993600-35994000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links