Variant report

Variant	rs1966384
Chromosome Location	chr10:116627910-116627911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10444099	1.00[JPT][hapmap]
rs1045657	1.00[JPT][hapmap]
rs1046492	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][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	0.92[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	0.88[CEU][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];0.96[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	0.84[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];0.96[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]
rs17092542	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]
rs17586888	0.82[AFR][1000 genomes]
rs17663670	1.00[ASW][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs17721283	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][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	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	1.00[JPT][hapmap]
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];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs2420069	1.00[ASW][hapmap];0.85[LWK][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	0.92[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	0.92[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]
rs7093674	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094072	0.88[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	0.84[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	0.91[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	0.92[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	0.91[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];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1966384	FAM160B1	cis	Adipose Subcutaneous	GTEx
rs1966384	TRUB1	cis	lesional skin	skin_eQTL
rs1966384	KIAA1600	cis	multi-tissue	Pritchard
rs1966384	FAM160B1	cis	Liver	GTEx
rs1966384	DCP1A	cis	Brain Pons	GTEx

Chromatin state (count:90 , 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	chr10:116610400-116628000	Weak transcription	Esophagus	oesophagus
6	chr10:116610600-116628000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr10:116611600-116641000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:116614800-116628400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:116617000-116630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr10:116617400-116640600	Weak transcription	Fetal Intestine Small	intestine
11	chr10:116619400-116634400	Weak transcription	Fetal Brain Male	brain
12	chr10:116619400-116636000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:116619400-116636400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr10:116619400-116641600	Weak transcription	Aorta	Aorta
15	chr10:116619800-116629400	Weak transcription	Colon Smooth Muscle	Colon
16	chr10:116619800-116634800	Weak transcription	Fetal Brain Female	brain
17	chr10:116620600-116635000	Weak transcription	Fetal Stomach	stomach
18	chr10:116621200-116629800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:116621400-116634800	Weak transcription	HepG2	liver
20	chr10:116621400-116636000	Weak transcription	Right Ventricle	heart
21	chr10:116621600-116628000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr10:116621600-116629400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:116621800-116639600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr10:116621800-116639600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:116622000-116639200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr10:116622200-116639000	Weak transcription	A549	lung
27	chr10:116622600-116628000	Weak transcription	HMEC	breast
28	chr10:116622600-116628000	Weak transcription	NHLF	lung
29	chr10:116622600-116631000	Weak transcription	Fetal Muscle Leg	muscle
30	chr10:116622600-116636800	Weak transcription	Brain Germinal Matrix	brain
31	chr10:116622800-116628000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr10:116622800-116628000	Weak transcription	NHEK	skin
33	chr10:116622800-116628400	Weak transcription	Hela-S3	cervix
34	chr10:116622800-116629400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:116622800-116636400	Weak transcription	Ovary	ovary
36	chr10:116623000-116634600	Weak transcription	Fetal Intestine Large	intestine
37	chr10:116623000-116634800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr10:116623800-116629600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:116623800-116634600	Weak transcription	GM12878-XiMat	blood
40	chr10:116624000-116634400	Weak transcription	Fetal Thymus	thymus
41	chr10:116624400-116629000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr10:116624400-116629200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr10:116624400-116629400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr10:116624400-116634600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr10:116624400-116635000	Weak transcription	Brain Hippocampus Middle	brain
46	chr10:116624400-116636800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:116624400-116639200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:116624600-116628600	Weak transcription	NH-A	brain
49	chr10:116624600-116634600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr10:116624600-116634600	Weak transcription	Fetal Kidney	kidney

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