Variant report

Variant	rs13299627
Chromosome Location	chr9:100025540-100025541
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10119245	0.80[EUR][1000 genomes]
rs10122063	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10125198	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10435868	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10448274	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10817265	0.84[EUR][1000 genomes]
rs10981209	0.83[EUR][1000 genomes]
rs10981280	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10981288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10981296	0.89[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10981438	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981890	0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap]
rs11581	0.86[JPT][hapmap]
rs11791310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11794422	0.80[EUR][1000 genomes]
rs11998999	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12004930	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12005128	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12235305	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12235734	0.84[EUR][1000 genomes]
rs13297670	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13298346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13301357	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13302699	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1544203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1903635	0.81[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1947717	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2169456	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2219664	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2242187	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2306097	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2493442	0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2493443	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2502644	0.82[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2615143	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2615145	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2795365	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2795367	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2818238	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2818239	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2818243	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28846196	0.85[EUR][1000 genomes]
rs3214072	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34382632	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34955252	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35609998	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3747489	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3747493	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs3747496	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3957904	0.85[EUR][1000 genomes]
rs3994556	0.85[EUR][1000 genomes]
rs4237189	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4284138	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4313271	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4366181	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs4523384	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4523385	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4626726	0.83[EUR][1000 genomes]
rs4743072	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4743076	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs4743077	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs4743084	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs55694850	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6478020	0.80[EUR][1000 genomes]
rs6478095	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7020393	0.91[JPT][hapmap]
rs7042707	0.91[JPT][hapmap]
rs713066	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72747776	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7470446	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs750674	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7856924	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7869959	0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13299627	VN1R51P	cis	Thyroid	GTEx
rs13299627	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:32 , 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	chr9:100002000-100037400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:100002000-100037800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:100002000-100038600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr9:100002000-100038600	Weak transcription	Fetal Intestine Large	intestine
7	chr9:100002000-100038600	Weak transcription	Fetal Intestine Small	intestine
8	chr9:100002000-100038800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:100002000-100038800	Weak transcription	Ovary	ovary
10	chr9:100002000-100038800	Weak transcription	Right Ventricle	heart
11	chr9:100002000-100039000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:100002000-100039600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:100002000-100039600	Weak transcription	Adipose Nuclei	Adipose
14	chr9:100002000-100039600	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:100002000-100039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr9:100002000-100040400	Weak transcription	Spleen	Spleen
17	chr9:100002200-100038800	Weak transcription	Liver	Liver
18	chr9:100002200-100039400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr9:100002200-100039400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:100002400-100037400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr9:100010600-100039400	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:100011600-100038800	Weak transcription	Fetal Stomach	stomach
23	chr9:100011600-100039600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:100013000-100040400	Weak transcription	Brain Substantia Nigra	brain
25	chr9:100022600-100039000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:100023400-100039600	Weak transcription	Fetal Lung	lung
27	chr9:100023600-100032800	Weak transcription	K562	blood
28	chr9:100024400-100040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:100024400-100042600	Weak transcription	Fetal Heart	heart
30	chr9:100025000-100039400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:100025400-100025800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:100025400-100025800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links