Variant report

Variant	rs7545806
Chromosome Location	chr1:166938555-166938556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1041238	0.84[CHD][hapmap]
rs10800276	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs10918599	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10918600	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10918603	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918607	0.82[ASW][hapmap];0.94[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs11576904	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11578336	0.87[CHD][hapmap];1.00[GIH][hapmap]
rs11579987	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11588176	0.92[ASN][1000 genomes]
rs12133327	0.84[CHD][hapmap]
rs12134016	0.83[CHD][hapmap]
rs12569084	1.00[GIH][hapmap]
rs2038020	0.83[ASN][1000 genomes]
rs2038022	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2072742	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142615	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2235184	0.88[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2280995	0.85[TSI][hapmap]
rs2294220	0.89[ASN][1000 genomes]
rs2312675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3736988	0.84[CHD][hapmap]
rs4657613	0.83[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs61815130	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61815132	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6427047	0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427048	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6427053	0.84[CHD][hapmap]
rs6660048	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs6669886	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs6673622	0.83[CHD][hapmap]
rs6673720	0.84[CHD][hapmap]
rs6677644	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6695162	1.00[GIH][hapmap]
rs6695609	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6699159	1.00[GIH][hapmap]
rs742048	0.82[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7518155	1.00[GIH][hapmap]
rs7520897	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7528849	1.00[GIH][hapmap]
rs7533688	1.00[GIH][hapmap]
rs7545911	1.00[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7545806	RGS4	cis	parietal	SCAN
rs7545806	FAM78B	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166927400-166941600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:166927600-166940200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:166927800-166940000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:166936600-166941600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:166936800-166940200	Weak transcription	Fetal Heart	heart
6	chr1:166937600-166939800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:166937600-166942200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:166937800-166941000	Enhancers	Primary T cells from cord blood	blood
9	chr1:166938000-166938800	Enhancers	Fetal Thymus	thymus
10	chr1:166938000-166939000	Enhancers	Thymus	Thymus
11	chr1:166938000-166940200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:166938400-166939200	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:166938400-166939200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:166938400-166939200	Flanking Active TSS	Dnd41	blood
15	chr1:166938400-166939400	Flanking Active TSS	GM12878-XiMat	blood

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