Variant report

Variant	rs12552101
Chromosome Location	chr9:100150285-100150286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100150282..100151155-chr9:100159898..100160560,2	MCF-7	breast:
2	chr9:100149689..100151422-chr9:100157235..100158759,2	MCF-7	breast:
3	chr9:100149125..100151047-chr9:100151218..100153967,3	K562	blood:
4	chr9:100149125..100152015-chr9:100152467..100154475,2	K562	blood:
5	chr9:100149625..100153516-chr9:100159731..100163036,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228957	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1048451	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10817337	0.81[EUR][1000 genomes]
rs10817384	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10817491	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817504	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10981367	0.82[EUR][1000 genomes]
rs10981444	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10981460	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981688	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10981701	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10981784	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10981800	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10981801	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1123379	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11581	0.95[EUR][1000 genomes]
rs12115447	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12115448	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12377538	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12378350	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12550923	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12551740	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12551818	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12552659	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12553155	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12553213	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12553259	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12554363	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12555277	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13285567	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13286510	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13287082	0.81[EUR][1000 genomes]
rs13289134	0.82[EUR][1000 genomes]
rs13289813	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13292715	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13300328	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13301045	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13301965	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1531440	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564048	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1564050	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16919506	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16919656	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16919661	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16919671	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16919675	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2045729	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2045730	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2045731	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2279113	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290933	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2306090	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2306092	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2306094	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2401384	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34135027	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34183765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34355647	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34476799	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34564795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34609282	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34616426	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34754033	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34870571	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34905303	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34954690	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35066943	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35123877	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35534888	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35590659	0.82[EUR][1000 genomes]
rs35623544	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35737497	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35778461	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35778718	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35788892	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747490	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747491	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747492	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747495	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3747498	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3747499	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3747504	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3747506	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3747507	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3747510	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3747511	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3827484	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3827485	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3994560	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41316960	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742686	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4742688	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743069	0.80[EUR][1000 genomes]
rs4743070	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4743073	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743082	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743083	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743085	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743086	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60681062	0.81[EUR][1000 genomes]
rs62556659	0.81[EUR][1000 genomes]
rs62557460	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62557461	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62557462	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62557463	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7020530	0.82[EUR][1000 genomes]
rs7038496	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7041222	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73565808	0.94[EUR][1000 genomes]
rs7872669	0.80[EUR][1000 genomes]
rs7874652	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs898869	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs898870	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9696058	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12552101	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100141200-100150800	Weak transcription	Lung	lung
2	chr9:100148400-100151200	Enhancers	Pancreas	Pancrea
3	chr9:100148800-100151200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr9:100148800-100151200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:100149000-100150800	Enhancers	GM12878-XiMat	blood
6	chr9:100149200-100150600	Enhancers	Fetal Brain Male	brain
7	chr9:100149200-100150800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr9:100149200-100151600	Enhancers	Primary B cells from peripheral blood	blood
9	chr9:100149200-100151800	Enhancers	Spleen	Spleen
10	chr9:100149200-100152000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:100149400-100150400	Enhancers	Right Ventricle	heart
12	chr9:100149400-100151800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr9:100149400-100152000	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr9:100149600-100150800	Weak transcription	Primary B cells from cord blood	blood
15	chr9:100149600-100154400	Weak transcription	Gastric	stomach
16	chr9:100149600-100161400	Weak transcription	Right Atrium	heart
17	chr9:100149800-100150400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:100149800-100150600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:100149800-100150800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:100149800-100150800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:100149800-100150800	Enhancers	Fetal Intestine Small	intestine
22	chr9:100149800-100150800	Weak transcription	Fetal Thymus	thymus
23	chr9:100149800-100151000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr9:100149800-100151000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:100149800-100151600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:100150000-100150400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr9:100150000-100150400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr9:100150000-100150400	Enhancers	Colonic Mucosa	Colon
29	chr9:100150000-100150600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
30	chr9:100150000-100150600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:100150000-100150800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:100150000-100151000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:100150000-100151200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:100150000-100151600	Enhancers	Duodenum Mucosa	Duodenum
35	chr9:100150200-100151000	Flanking Active TSS	HepG2	liver

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