Variant report

Variant	rs3862899
Chromosome Location	chr1:76756343-76756344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11162114	0.81[EUR][1000 genomes]
rs11162115	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12071138	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12124295	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124554	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125121	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125168	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127441	0.81[EUR][1000 genomes]
rs12127832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131613	0.88[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1360878	0.81[CEU][hapmap]
rs1414482	0.81[CEU][hapmap]
rs1537783	0.92[CEU][hapmap]
rs17670910	0.87[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17671689	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2065793	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2210832	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2893415	0.92[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs35517533	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3862900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4083857	0.81[CEU][hapmap]
rs4262595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4290109	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4290110	1.00[YRI][hapmap]
rs4480406	0.81[CEU][hapmap]
rs4607942	0.81[CEU][hapmap]
rs55805865	0.81[EUR][1000 genomes]
rs55813741	0.80[EUR][1000 genomes]
rs55930988	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60579420	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6672694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691694	0.80[EUR][1000 genomes]
rs6694998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6697478	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72675958	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72675960	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72675971	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9437395	0.81[CEU][hapmap]
rs9437408	0.92[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][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	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3862899	ELTD1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76745600-76761000	Weak transcription	Aorta	Aorta
2	chr1:76747600-76756400	Weak transcription	Fetal Brain Male	brain
3	chr1:76747600-76757000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:76747800-76756400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:76749200-76760000	Enhancers	Primary T cells from cord blood	blood
6	chr1:76750200-76760200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:76750400-76757200	Enhancers	Fetal Thymus	thymus
8	chr1:76750400-76760200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:76750400-76760600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr1:76750400-76762000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:76751000-76756400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:76751800-76757600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:76753600-76760200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:76754000-76758600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:76754000-76761600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:76754600-76756400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:76755000-76756600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:76755200-76756400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:76755200-76757200	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr1:76755400-76756600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:76755400-76756600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr1:76755400-76756600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:76755400-76756800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:76755400-76757200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:76755400-76757200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:76755400-76758000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:76755600-76756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:76755600-76757800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:76755800-76783000	Weak transcription	Fetal Lung	lung
30	chr1:76756000-76756800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr1:76756000-76757200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:76756000-76758800	Enhancers	Primary B cells from cord blood	blood
33	chr1:76756200-76756400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:76756200-76756400	Enhancers	Thymus	Thymus
35	chr1:76756200-76756800	Enhancers	Brain Hippocampus Middle	brain
36	chr1:76756200-76757000	Enhancers	Primary B cells from peripheral blood	blood
37	chr1:76756200-76757200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr1:76756200-76757200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:76756200-76757200	Enhancers	Fetal Muscle Leg	muscle
40	chr1:76756200-76757200	Enhancers	Fetal Stomach	stomach
41	chr1:76756200-76757400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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