Variant report

Variant	rs12550923
Chromosome Location	chr9:100023393-100023394
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1048451	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10521029	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10817337	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817384	0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10817491	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs10817504	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10981297	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10981367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981434	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981444	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10981460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10981688	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10981701	0.83[ASN][1000 genomes]
rs10981784	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10981800	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10981801	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10981931	0.85[JPT][hapmap]
rs1123379	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11581	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12115447	0.85[EUR][1000 genomes]
rs12115448	0.83[EUR][1000 genomes]
rs12377538	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12378350	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12551740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12551818	0.82[EUR][1000 genomes]
rs12552101	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12552659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12553155	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12553213	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12553259	0.84[EUR][1000 genomes]
rs12554363	0.94[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12554887	0.83[AMR][1000 genomes]
rs12555277	0.94[CEU][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13285567	0.87[CEU][hapmap]
rs13286510	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13287082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13289134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13289813	0.94[CEU][hapmap]
rs13292715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300328	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs13301045	0.93[CEU][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13301965	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1531440	0.94[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1542506	0.81[JPT][hapmap]
rs1564048	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1564050	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16919506	0.82[EUR][1000 genomes]
rs16919656	0.81[EUR][1000 genomes]
rs16919661	0.84[EUR][1000 genomes]
rs16919671	0.85[EUR][1000 genomes]
rs16919675	0.89[CEU][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs1986462	0.94[CEU][hapmap]
rs2045729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2045730	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2045731	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2279113	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290933	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306090	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2306092	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2306094	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2401384	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34135027	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34183765	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34355647	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34476799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34564795	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34609282	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34616426	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34754033	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34870571	0.85[EUR][1000 genomes]
rs34905303	0.82[EUR][1000 genomes]
rs34954690	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35066943	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35123877	0.83[EUR][1000 genomes]
rs35534888	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35590659	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35623544	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35737497	0.85[EUR][1000 genomes]
rs35778461	0.80[EUR][1000 genomes]
rs35778718	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35788892	0.82[EUR][1000 genomes]
rs3747490	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3747491	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3747492	0.94[CEU][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3747495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3747498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3747499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3747504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3747506	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3747507	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3747510	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3747511	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3827484	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3827485	0.83[EUR][1000 genomes]
rs3994560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4128763	1.00[CEU][hapmap]
rs41316960	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742686	0.88[CEU][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4742688	0.94[CEU][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4742689	0.84[JPT][hapmap]
rs4743069	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743073	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743082	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743083	1.00[CEU][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743085	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743086	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743088	0.85[JPT][hapmap]
rs60681062	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62556659	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62557460	0.83[EUR][1000 genomes]
rs62557461	0.83[EUR][1000 genomes]
rs62557462	0.84[EUR][1000 genomes]
rs62557463	0.84[EUR][1000 genomes]
rs62559861	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478038	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6478039	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7020530	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7038496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7041222	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73565808	0.80[EUR][1000 genomes]
rs7872669	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7874652	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs898869	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs898870	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs9696058	0.83[AMR][1000 genomes];0.82[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	nsv972791	chr9:100007482-100037888	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12550923	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100001200-100039400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:100001600-100037400	Weak transcription	Primary T cells from cord blood	blood
3	chr9:100002000-100025400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:100002000-100037400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:100002000-100037800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:100002000-100038600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:100002000-100038600	Weak transcription	Fetal Intestine Large	intestine
8	chr9:100002000-100038600	Weak transcription	Fetal Intestine Small	intestine
9	chr9:100002000-100038800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr9:100002000-100038800	Weak transcription	Ovary	ovary
11	chr9:100002000-100038800	Weak transcription	Right Ventricle	heart
12	chr9:100002000-100039000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:100002000-100039600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:100002000-100039600	Weak transcription	Adipose Nuclei	Adipose
15	chr9:100002000-100039600	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:100002000-100039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:100002000-100040400	Weak transcription	Spleen	Spleen
18	chr9:100002200-100038800	Weak transcription	Liver	Liver
19	chr9:100002200-100039400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:100002200-100039400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:100002400-100037400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr9:100010600-100039400	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:100011600-100038800	Weak transcription	Fetal Stomach	stomach
24	chr9:100011600-100039600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:100013000-100040400	Weak transcription	Brain Substantia Nigra	brain
26	chr9:100021400-100025400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:100022200-100023600	Enhancers	K562	blood
28	chr9:100022600-100039000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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