Variant report

Variant	rs13287082
Chromosome Location	chr9:100011240-100011241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1048451	1.00[CEU][hapmap]
rs10521029	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10817337	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10817384	0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10817491	0.94[CEU][hapmap]
rs10817504	0.84[CEU][hapmap]
rs10981297	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10981367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10981460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10981688	0.81[EUR][1000 genomes]
rs10981784	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs10981800	0.94[CEU][hapmap]
rs10981931	0.85[JPT][hapmap]
rs11581	1.00[CEU][hapmap]
rs12115447	0.81[EUR][1000 genomes]
rs12377538	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12378350	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12550923	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]
rs12551740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12552101	0.81[EUR][1000 genomes]
rs12552659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12553155	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12553213	1.00[CEU][hapmap]
rs12554363	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs12554887	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12555277	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs13285567	0.87[CEU][hapmap]
rs13286510	0.94[CEU][hapmap]
rs13289134	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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13289813	0.94[CEU][hapmap]
rs13292715	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13300328	0.94[CEU][hapmap]
rs13301045	0.94[CEU][hapmap];0.83[YRI][hapmap]
rs13301965	0.81[EUR][1000 genomes]
rs1531440	0.94[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs1542506	0.81[JPT][hapmap]
rs1564048	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs16919671	0.81[EUR][1000 genomes]
rs16919675	0.89[CEU][hapmap];0.81[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];0.81[EUR][1000 genomes]
rs2045730	1.00[CEU][hapmap]
rs2045731	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs2279113	0.81[EUR][1000 genomes]
rs2290933	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2306090	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs2306092	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs2306094	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2401384	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs34135027	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34183765	0.81[EUR][1000 genomes]
rs34355647	0.82[EUR][1000 genomes]
rs34476799	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34564795	0.81[EUR][1000 genomes]
rs34616426	0.81[EUR][1000 genomes]
rs34754033	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34870571	0.81[EUR][1000 genomes]
rs35590659	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35737497	0.81[EUR][1000 genomes]
rs3747490	0.94[CEU][hapmap]
rs3747491	0.94[CEU][hapmap]
rs3747492	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs3747495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3747498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3747499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs3747504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3747506	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3747507	0.81[EUR][1000 genomes]
rs3747511	0.81[EUR][1000 genomes]
rs3994560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4128763	1.00[CEU][hapmap]
rs41316960	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4742686	0.83[YRI][hapmap]
rs4742688	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs4742689	0.84[JPT][hapmap]
rs4743069	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743070	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]
rs4743073	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4743082	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4743083	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs4743085	0.94[CEU][hapmap]
rs4743086	0.94[CEU][hapmap]
rs4743088	0.85[JPT][hapmap]
rs60681062	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62556659	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559861	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6478038	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6478039	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7020530	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7038496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7041222	0.94[CEU][hapmap]
rs7872669	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs898869	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs898870	1.00[CEU][hapmap];0.85[YRI][hapmap]

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
rs13287082	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100001200-100017000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:100001200-100039400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:100001400-100014000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr9:100001400-100017600	Weak transcription	Left Ventricle	heart
5	chr9:100001400-100017800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:100001600-100012800	Weak transcription	Fetal Kidney	kidney
7	chr9:100001600-100014000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:100001600-100022200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:100001600-100037400	Weak transcription	Primary T cells from cord blood	blood
10	chr9:100001800-100012800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:100002000-100011600	Weak transcription	Pancreas	Pancrea
12	chr9:100002000-100013200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:100002000-100013400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:100002000-100015200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:100002000-100016600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:100002000-100016600	Weak transcription	Thymus	Thymus
17	chr9:100002000-100018000	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:100002000-100023000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:100002000-100025400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:100002000-100037400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:100002000-100037800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:100002000-100038600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:100002000-100038600	Weak transcription	Fetal Intestine Large	intestine
24	chr9:100002000-100038600	Weak transcription	Fetal Intestine Small	intestine
25	chr9:100002000-100038800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr9:100002000-100038800	Weak transcription	Ovary	ovary
27	chr9:100002000-100038800	Weak transcription	Right Ventricle	heart
28	chr9:100002000-100039000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr9:100002000-100039600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr9:100002000-100039600	Weak transcription	Adipose Nuclei	Adipose
31	chr9:100002000-100039600	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:100002000-100039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:100002000-100040400	Weak transcription	Spleen	Spleen
34	chr9:100002200-100013000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:100002200-100014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:100002200-100038800	Weak transcription	Liver	Liver
37	chr9:100002200-100039400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr9:100002200-100039400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:100002400-100037400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr9:100003200-100017600	Weak transcription	Dnd41	blood
41	chr9:100009200-100015800	Weak transcription	Psoas Muscle	Psoas
42	chr9:100010000-100015800	Weak transcription	Esophagus	oesophagus
43	chr9:100010200-100011600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:100010600-100011600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:100010600-100039400	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:100010800-100011400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:100010800-100018000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:100011000-100011400	ZNF genes & repeats	Lung	lung
49	chr9:100011000-100011600	Strong transcription	Fetal Stomach	stomach
50	chr9:100011000-100012600	Weak transcription	Brain Angular Gyrus	brain

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