Variant report

Variant	rs71459334
Chromosome Location	chr12:56434210-56434211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr12:56434066-56434258	MCF10A-Er-Src	breast:	n/a	chr12:56434131-56434143 chr12:56434134-56434141 chr12:56434132-56434141

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56434197..56436008-chr12:56614741..56617329,2	K562	blood:
2	chr12:56359758..56363158-chr12:56433727..56437301,5	K562	blood:
3	chr12:56433777..56443620-chr12:56502225..56514736,38	MCF-7	breast:
4	chr12:56318003..56321783-chr12:56433300..56437111,4	K562	blood:
5	chr12:56137085..56138942-chr12:56433980..56436388,2	K562	blood:
6	chr12:56434034..56442629-chr12:56495467..56501430,16	MCF-7	breast:
7	chr12:56417053..56422414-chr12:56432550..56437155,7	K562	blood:
8	chr12:56398217..56408038-chr12:56433794..56439966,15	K562	blood:
9	chr12:56421691..56428762-chr12:56433229..56437460,13	MCF-7	breast:
10	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:
11	chr12:56399898..56405642-chr12:56433175..56438589,7	K562	blood:
12	chr12:56363397..56371565-chr12:56432514..56437993,13	K562	blood:
13	chr12:56434164..56442518-chr12:56471459..56476251,24	MCF-7	breast:
14	chr12:56433873..56442113-chr12:56515349..56524351,14	K562	blood:
15	chr12:56431889..56443161-chr12:56494616..56500426,22	MCF-7	breast:
16	chr12:56434006..56443603-chr12:56507645..56514884,44	K562	blood:
17	chr12:56364726..56370308-chr12:56432734..56438629,15	K562	blood:
18	chr12:56434062..56437733-chr12:56543304..56547386,5	K562	blood:
19	chr12:56073598..56075445-chr12:56433762..56436346,2	K562	blood:
20	chr12:56222083..56225232-chr12:56434095..56438071,8	MCF-7	breast:
21	chr12:56320184..56328034-chr12:56431937..56442233,20	MCF-7	breast:
22	chr12:56433331..56443603-chr12:56506173..56514581,35	K562	blood:
23	chr12:56364512..56372057-chr12:56434108..56438254,11	MCF-7	breast:
24	chr12:56331445..56332986-chr12:56434203..56437015,2	MCF-7	breast:
25	chr12:56433732..56435400-chr12:56549720..56552057,2	K562	blood:
26	chr12:56434140..56437753-chr12:56579716..56586472,8	K562	blood:
27	chr12:56388988..56394527-chr12:56433794..56442585,20	K562	blood:
28	chr12:56413395..56415728-chr12:56433870..56436812,2	K562	blood:
29	chr12:56386022..56392601-chr12:56434180..56439537,11	MCF-7	breast:
30	chr12:56434092..56435829-chr12:56551661..56553282,2	K562	blood:
31	chr12:56389319..56393039-chr12:56433877..56439169,10	K562	blood:
32	chr12:56399605..56402732-chr12:56433705..56437280,6	MCF-7	breast:
33	chr12:56433908..56446518-chr12:56506026..56517165,55	MCF-7	breast:

No data

Variant related genes	Relation type
RPS26	TF binding region
ENSG00000170473	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000257384	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258056	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11171713	0.93[AMR][1000 genomes]
rs11171714	0.93[AMR][1000 genomes]
rs11171715	0.82[AMR][1000 genomes]
rs12099979	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12810011	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12815302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12815387	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12815488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12817471	0.85[EUR][1000 genomes]
rs12817765	0.93[AMR][1000 genomes]
rs12818756	1.00[EUR][1000 genomes]
rs12831468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1614219	0.98[EUR][1000 genomes]
rs1689511	0.95[EUR][1000 genomes]
rs1701706	0.91[EUR][1000 genomes]
rs17118206	0.93[AMR][1000 genomes]
rs17118208	0.93[AMR][1000 genomes]
rs17118262	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131569	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2456972	0.98[EUR][1000 genomes]
rs2658479	0.94[EUR][1000 genomes]
rs34071823	0.93[AMR][1000 genomes]
rs34228181	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34273234	0.87[AMR][1000 genomes]
rs34303864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34406511	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34485293	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34507011	0.91[EUR][1000 genomes]
rs34602183	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34650555	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34921584	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34962186	0.93[AMR][1000 genomes]
rs35485002	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35662491	0.85[EUR][1000 genomes]
rs35666826	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35961650	0.94[EUR][1000 genomes]
rs4759022	1.00[EUR][1000 genomes]
rs4759239	0.94[EUR][1000 genomes]
rs67594137	0.87[AMR][1000 genomes]
rs71447768	0.93[AMR][1000 genomes]
rs71459326	0.93[AMR][1000 genomes]
rs71459327	0.93[AMR][1000 genomes]
rs71459336	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71459339	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459342	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7298818	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7300772	0.98[EUR][1000 genomes]
rs772919	0.89[EUR][1000 genomes]
rs772922	0.91[EUR][1000 genomes]
rs772923	0.92[EUR][1000 genomes]
rs773115	0.94[EUR][1000 genomes]
rs7963590	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7977537	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv1067906	chr12:56424828-56445284	Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71459334	SUOX	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56402200-56434800	Weak transcription	Psoas Muscle	Psoas
2	chr12:56409400-56435000	Weak transcription	Stomach Mucosa	stomach
3	chr12:56416000-56434800	Weak transcription	Primary B cells from cord blood	blood
4	chr12:56416000-56434800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:56416000-56435000	Weak transcription	Right Atrium	heart
6	chr12:56416200-56434800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:56421800-56434600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:56423600-56434400	Weak transcription	HMEC	breast
9	chr12:56423600-56434800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:56423600-56434800	Weak transcription	NH-A	brain
11	chr12:56426200-56434600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:56427000-56434600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:56427000-56434600	Weak transcription	NHLF	lung
14	chr12:56427200-56434800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:56427200-56434800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:56427200-56434800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:56427200-56434800	Weak transcription	Thymus	Thymus
18	chr12:56427200-56434800	Weak transcription	HSMM	muscle
19	chr12:56427200-56435000	Weak transcription	Small Intestine	intestine
20	chr12:56429000-56434600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:56429000-56434800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr12:56429000-56434800	Weak transcription	HSMMtube	muscle
23	chr12:56429200-56434800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:56429200-56434800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:56429200-56434800	Weak transcription	Osteobl	bone
26	chr12:56429200-56435000	Weak transcription	Pancreas	Pancrea
27	chr12:56429200-56435600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:56429400-56434600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:56429400-56434800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:56429400-56435000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:56429400-56435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:56429400-56435000	Weak transcription	Esophagus	oesophagus
33	chr12:56429400-56435600	Weak transcription	Gastric	stomach
34	chr12:56429600-56434800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:56429600-56434800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr12:56429800-56434400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:56429800-56434600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:56429800-56434600	Weak transcription	Fetal Kidney	kidney
39	chr12:56429800-56434800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:56429800-56434800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:56430000-56434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:56430000-56434600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:56430200-56434600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr12:56430200-56434600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:56430200-56435600	Weak transcription	Spleen	Spleen
46	chr12:56430400-56434600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:56430400-56434800	Weak transcription	Brain Substantia Nigra	brain
48	chr12:56430400-56435000	Weak transcription	Right Ventricle	heart
49	chr12:56430600-56434400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:56430600-56434800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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