Variant report

Variant	rs9437408
Chromosome Location	chr1:76755163-76755164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11162109	0.82[ASN][1000 genomes]
rs11162114	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162115	0.80[EUR][1000 genomes]
rs12124295	0.81[EUR][1000 genomes]
rs12124554	0.92[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs12125121	0.81[EUR][1000 genomes]
rs12125168	0.81[EUR][1000 genomes]
rs12126170	0.80[EUR][1000 genomes]
rs12127441	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127832	0.81[EUR][1000 genomes]
rs12131613	0.81[CEU][hapmap]
rs1335862	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1335863	0.81[ASN][1000 genomes]
rs1335864	0.81[ASN][1000 genomes]
rs1360878	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1414476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414479	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1414480	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1414481	0.98[ASN][1000 genomes]
rs1414482	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1414483	0.89[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1414484	0.85[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1414485	0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1414487	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs1537783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537784	0.82[JPT][hapmap]
rs17098538	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs17670910	0.81[CEU][hapmap]
rs2065794	0.85[ASN][1000 genomes]
rs2067914	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2225784	0.81[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs2392036	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2893415	0.85[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3851267	0.82[JPT][hapmap]
rs3862899	0.92[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs3862900	0.92[CEU][hapmap]
rs3862901	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3883995	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3891339	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3904687	0.82[JPT][hapmap]
rs3920772	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4083857	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4086568	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4245648	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4262595	0.80[EUR][1000 genomes]
rs4300269	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4480406	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4607942	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949700	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949702	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949703	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55805865	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55813741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593527	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs6657540	0.81[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs6672694	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs6675148	0.90[ASN][1000 genomes]
rs6691694	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694998	0.80[EUR][1000 genomes]
rs6695042	0.80[ASN][1000 genomes]
rs6697478	0.92[CEU][hapmap]
rs6700436	0.98[ASN][1000 genomes]
rs6702605	0.92[ASN][1000 genomes]
rs7516589	0.80[ASN][1000 genomes]
rs7534588	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9437395	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9437402	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9437407	0.82[CHD][hapmap];0.82[JPT][hapmap]

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
rs9437408	ELTD1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76745600-76761000	Weak transcription	Aorta	Aorta
2	chr1:76745800-76755400	Weak transcription	Fetal Lung	lung
3	chr1:76747400-76756200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:76747600-76756400	Weak transcription	Fetal Brain Male	brain
5	chr1:76747600-76757000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:76747800-76756200	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:76747800-76756400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:76749200-76760000	Enhancers	Primary T cells from cord blood	blood
9	chr1:76750200-76760200	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr1:76750400-76757200	Enhancers	Fetal Thymus	thymus
11	chr1:76750400-76760200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:76750400-76760600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr1:76750400-76762000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:76750800-76755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:76751000-76755200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:76751000-76756400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:76751200-76755400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:76751800-76757600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:76752000-76755200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:76752200-76756000	Weak transcription	Primary B cells from cord blood	blood
21	chr1:76753600-76755400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:76753600-76760200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:76754000-76758600	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:76754000-76761600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr1:76754600-76756400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:76755000-76755200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:76755000-76755600	Enhancers	Thymus	Thymus
28	chr1:76755000-76756600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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