Variant report

Variant	rs2106084
Chromosome Location	chr1:158391426-158391427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10489829	0.82[ASN][1000 genomes]
rs10489830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10489831	0.81[JPT][hapmap]
rs10908649	0.81[ASN][1000 genomes]
rs1119029	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264971	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12118413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12119297	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12122595	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12125990	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12127971	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12129036	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12132792	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12133777	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12134692	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12136746	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12136971	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12138872	0.82[ASN][1000 genomes]
rs12139611	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12141446	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12141449	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12142715	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12143038	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12144696	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12145637	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12239443	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12725399	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12725721	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12728815	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12729052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12738597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs12742451	0.84[ASN][1000 genomes]
rs12743143	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12743313	0.82[ASN][1000 genomes]
rs12744495	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12747451	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1321647	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13375849	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13376086	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1342937	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1342938	0.83[ASN][1000 genomes]
rs1342939	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1342940	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1342941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1342942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1388267	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1418841	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1418842	0.93[CEU][hapmap]
rs1546064	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1578759	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1578760	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17627697	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17627858	0.82[ASN][1000 genomes]
rs17628151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17628749	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17678931	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17679007	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1894039	0.81[JPT][hapmap]
rs1907467	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2188102	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2188107	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2188108	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2201059	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2213946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2220630	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34199939	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34246317	0.81[ASN][1000 genomes]
rs34443037	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34616883	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34959155	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35053382	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35321102	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35358362	0.81[ASN][1000 genomes]
rs35430171	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35504011	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35963645	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4628505	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4644490	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4656284	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4656286	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56125590	0.81[ASN][1000 genomes]
rs56937999	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57472964	0.83[ASN][1000 genomes]
rs57525598	0.82[ASN][1000 genomes]
rs58605957	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59524892	0.81[ASN][1000 genomes]
rs60351230	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61034754	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6427437	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6660236	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6672590	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6675399	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6692530	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66946798	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6699757	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67317531	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7418542	0.80[ASN][1000 genomes]
rs7525550	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7540866	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs961562	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs977384	0.81[ASN][1000 genomes]
rs989203	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv831692	chr1:158223459-158392016	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv998569	chr1:158317392-158443389	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2106084	S100A4	cis	parietal	SCAN
rs2106084	KIRREL	cis	cerebellum	SCAN
rs2106084	SPRR2A	cis	parietal	SCAN
rs2106084	SLAMF9	cis	cerebellum	SCAN
rs2106084	C1orf68	cis	cerebellum	SCAN
rs2106084	TDRD10	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158383000-158391600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:158391000-158391800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr1:158391000-158392000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:158391400-158393000	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:158391400-158393000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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