Variant report

Variant	rs17009249
Chromosome Location	chr4:85667827-85667828
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKX6-1-8	chr4:85667306-85668442	l_2680_chr4:85667155-85670292_thyroid

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10007879	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11097024	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12511112	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13118671	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs13145705	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1385263	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1484661	0.91[JPT][hapmap]
rs1508670	0.81[JPT][hapmap]
rs17009168	0.86[MEX][hapmap]
rs17009247	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009317	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs17009334	0.90[JPT][hapmap]
rs17009341	0.87[JPT][hapmap];0.82[MEX][hapmap]
rs2046402	0.81[EUR][1000 genomes]
rs2046404	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2170935	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2218323	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2869216	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs3098928	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36036245	0.86[EUR][1000 genomes]
rs3747680	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs4529041	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6531775	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6531777	0.82[CHB][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap]
rs67045782	0.81[EUR][1000 genomes]
rs6825852	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs6829807	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs6835046	0.82[EUR][1000 genomes]
rs6838727	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs6839516	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847067	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6847564	0.95[JPT][hapmap]
rs6853486	0.88[CEU][hapmap];0.82[MEX][hapmap]
rs6858666	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72664926	0.82[EUR][1000 genomes]
rs7668460	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7685537	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv532738	chr4:85590841-85777997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17009249	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85604400-85674800	Weak transcription	Small Intestine	intestine
2	chr4:85615000-85677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:85619200-85726000	Weak transcription	Hela-S3	cervix
4	chr4:85636400-85701200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:85642800-85668000	Weak transcription	Spleen	Spleen
6	chr4:85642800-85678000	Weak transcription	Gastric	stomach
7	chr4:85648000-85676200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:85651000-85671400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:85651000-85673000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:85651000-85673200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:85651000-85676800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:85651000-85678600	Strong transcription	Placenta	Placenta
13	chr4:85652200-85670000	Strong transcription	Liver	Liver
14	chr4:85652200-85678400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:85652200-85678400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:85652200-85679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:85652400-85679200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:85652600-85671600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:85652600-85678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:85652600-85678600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:85655000-85668400	Weak transcription	Fetal Brain Male	brain
22	chr4:85656800-85672000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:85657000-85704200	Weak transcription	Psoas Muscle	Psoas
24	chr4:85657400-85671400	Strong transcription	HSMM	muscle
25	chr4:85658000-85673800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:85658000-85676600	Strong transcription	Fetal Intestine Large	intestine
27	chr4:85659200-85674200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:85659800-85678400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:85660400-85669200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:85660800-85668400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:85660800-85672200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:85661000-85668000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:85661000-85668200	Weak transcription	A549	lung
34	chr4:85661000-85669200	Weak transcription	Fetal Heart	heart
35	chr4:85661600-85668000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:85661600-85668200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:85661600-85668200	Weak transcription	Aorta	Aorta
38	chr4:85662200-85668600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:85662600-85670200	Strong transcription	NHDF-Ad	bronchial
40	chr4:85663200-85678400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:85663800-85670000	Weak transcription	Pancreas	Pancrea
42	chr4:85664000-85668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:85664000-85668000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:85664000-85668200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:85664000-85668200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:85664000-85668200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:85664000-85668200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr4:85664000-85668200	Weak transcription	Esophagus	oesophagus
49	chr4:85664000-85668200	Weak transcription	Fetal Intestine Small	intestine
50	chr4:85664000-85668200	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links