Variant report

Variant	rs17092542
Chromosome Location	chr10:116630289-116630290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116531753..116534346-chr10:116628137..116630750,2	K562	blood:

Extended variants
information (count: 127 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10444099	1.00[JPT][hapmap]
rs1045657	1.00[JPT][hapmap]
rs1046492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490909	0.82[ASW][hapmap];0.82[YRI][hapmap]
rs10510007	0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10885613	0.88[AFR][1000 genomes]
rs10885614	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs10885633	1.00[JPT][hapmap]
rs10885634	1.00[JPT][hapmap]
rs10885636	1.00[JPT][hapmap]
rs10885638	1.00[JPT][hapmap]
rs10885639	1.00[JPT][hapmap]
rs11196924	0.90[ASW][hapmap]
rs11196929	0.82[AFR][1000 genomes]
rs11196930	0.88[AFR][1000 genomes]
rs11196932	0.88[AFR][1000 genomes]
rs11196935	0.83[AFR][1000 genomes]
rs11196936	0.88[AFR][1000 genomes]
rs11196937	0.88[AFR][1000 genomes]
rs11196939	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs11196941	0.86[AFR][1000 genomes]
rs11196943	0.85[AFR][1000 genomes]
rs11196944	0.87[AFR][1000 genomes]
rs11196945	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs11196948	0.84[AFR][1000 genomes]
rs11196950	0.84[AFR][1000 genomes]
rs11196951	0.84[AFR][1000 genomes]
rs11196952	0.86[AFR][1000 genomes]
rs11196953	0.86[AFR][1000 genomes]
rs11196963	1.00[CHB][hapmap]
rs11196984	1.00[JPT][hapmap]
rs11196996	1.00[JPT][hapmap]
rs11196999	1.00[JPT][hapmap]
rs11197000	1.00[JPT][hapmap]
rs11197007	1.00[JPT][hapmap]
rs11197010	1.00[JPT][hapmap]
rs11197012	1.00[JPT][hapmap]
rs11818115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098332	1.00[JPT][hapmap]
rs12218498	0.87[AFR][1000 genomes]
rs12265048	1.00[JPT][hapmap]
rs12269261	1.00[JPT][hapmap]
rs12415173	0.90[AFR][1000 genomes]
rs12761122	1.00[JPT][hapmap]
rs12764662	1.00[JPT][hapmap]
rs12765350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771956	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772800	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775180	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359079	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs17092497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17586888	0.82[AFR][1000 genomes]
rs17663670	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs17721283	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17721905	1.00[JPT][hapmap]
rs17794346	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	1.00[JPT][hapmap]
rs1966384	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105001	1.00[JPT][hapmap]
rs2146805	0.85[AFR][1000 genomes]
rs2146806	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420065	0.88[AFR][1000 genomes]
rs2420066	0.88[AFR][1000 genomes]
rs2420067	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs2420069	1.00[ASW][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs3180654	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34064819	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34187191	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683721	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35010779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35622181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35628210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036948	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089581	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758603	0.86[AFR][1000 genomes]
rs41284358	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55711292	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58587374	0.85[AFR][1000 genomes]
rs60820172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61596353	0.84[AFR][1000 genomes]
rs61867965	0.87[AFR][1000 genomes]
rs61867966	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867967	1.00[ASN][1000 genomes]
rs61868018	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	1.00[JPT][hapmap]
rs6585310	1.00[JPT][hapmap]
rs6585311	1.00[JPT][hapmap]
rs68085797	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071789	1.00[JPT][hapmap]
rs7071812	1.00[JPT][hapmap]
rs7072356	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072364	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079877	0.86[AFR][1000 genomes]
rs7089973	0.83[CEU][hapmap]
rs7093674	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099565	1.00[JPT][hapmap]
rs7099590	1.00[JPT][hapmap]
rs7100026	1.00[JPT][hapmap]
rs749649	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897937	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs7898249	1.00[JPT][hapmap]
rs7903663	0.86[AFR][1000 genomes]
rs7904188	0.90[AFR][1000 genomes]
rs7904605	1.00[JPT][hapmap]
rs7908069	1.00[JPT][hapmap]
rs7908464	1.00[JPT][hapmap]
rs7909566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914792	0.88[AFR][1000 genomes]
rs7918253	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7918388	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919649	0.90[AFR][1000 genomes]
rs7920216	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs7923295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181444	0.88[AFR][1000 genomes]
rs881192	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17092542	DCP1A	cis	Brain Pons	GTEx
rs17092542	FAM160B1	cis	Adipose Subcutaneous	GTEx
rs17092542	TRUB1	cis	cerebellum	SCAN
rs17092542	ADRB1	cis	parietal	SCAN
rs17092542	TRUB1	cis	parietal	SCAN
rs17092542	TECTB	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116589600-116640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:116609600-116634800	Weak transcription	Spleen	Spleen
3	chr10:116609600-116639400	Weak transcription	Pancreas	Pancrea
4	chr10:116610200-116634600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr10:116611600-116641000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr10:116617400-116640600	Weak transcription	Fetal Intestine Small	intestine
7	chr10:116619400-116634400	Weak transcription	Fetal Brain Male	brain
8	chr10:116619400-116636000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:116619400-116636400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:116619400-116641600	Weak transcription	Aorta	Aorta
11	chr10:116619800-116634800	Weak transcription	Fetal Brain Female	brain
12	chr10:116620600-116635000	Weak transcription	Fetal Stomach	stomach
13	chr10:116621400-116634800	Weak transcription	HepG2	liver
14	chr10:116621400-116636000	Weak transcription	Right Ventricle	heart
15	chr10:116621800-116639600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr10:116621800-116639600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr10:116622000-116639200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr10:116622200-116639000	Weak transcription	A549	lung
19	chr10:116622600-116631000	Weak transcription	Fetal Muscle Leg	muscle
20	chr10:116622600-116636800	Weak transcription	Brain Germinal Matrix	brain
21	chr10:116622800-116636400	Weak transcription	Ovary	ovary
22	chr10:116623000-116634600	Weak transcription	Fetal Intestine Large	intestine
23	chr10:116623000-116634800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr10:116623800-116634600	Weak transcription	GM12878-XiMat	blood
25	chr10:116624000-116634400	Weak transcription	Fetal Thymus	thymus
26	chr10:116624400-116634600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:116624400-116635000	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:116624400-116636800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr10:116624400-116639200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:116624600-116634600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr10:116624600-116634600	Weak transcription	Fetal Kidney	kidney
32	chr10:116624800-116634600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr10:116624800-116636200	Weak transcription	Placenta	Placenta
34	chr10:116624800-116636600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:116624800-116636600	Weak transcription	Brain Anterior Caudate	brain
36	chr10:116625200-116634600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr10:116625400-116634000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr10:116625400-116634600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:116625400-116635000	Weak transcription	Fetal Lung	lung
40	chr10:116625400-116636200	Weak transcription	Liver	Liver
41	chr10:116625600-116632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:116625600-116634800	Weak transcription	Adipose Nuclei	Adipose
43	chr10:116625600-116635000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:116626200-116634200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr10:116626400-116634600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr10:116626600-116633800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr10:116627200-116630800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr10:116627400-116630400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:116627400-116631400	Enhancers	NHDF-Ad	bronchial
50	chr10:116627600-116634800	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links