Variant report

Variant	rs13388459
Chromosome Location	chr2:77215497-77215498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10172981	1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs10198799	0.82[TSI][hapmap]
rs10208087	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10520174	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap]
rs10520177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520179	0.83[CEU][hapmap];0.88[TSI][hapmap]
rs1075716	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077111	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892997	0.92[TSI][hapmap]
rs13383667	0.88[LWK][hapmap]
rs13413951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345137	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1446696	0.91[CEU][hapmap]
rs1446708	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1446721	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17013567	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17013635	0.91[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs17333696	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs17333850	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs17333884	0.85[CEU][hapmap]
rs17333926	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17334205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334506	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs17334527	0.91[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs17405711	0.85[CEU][hapmap]
rs17405724	0.85[CEU][hapmap]
rs17405864	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17405905	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs17406023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406084	0.92[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs17406091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17406374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17406395	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs17406416	0.91[CEU][hapmap]
rs17406465	0.83[CEU][hapmap];0.88[TSI][hapmap]
rs1960005	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2077823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34007251	0.84[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs4396752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491748	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4637153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853285	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap]
rs55800138	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55864802	0.87[EUR][1000 genomes]
rs56055201	0.82[EUR][1000 genomes]
rs62170208	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170209	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62170210	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170337	0.90[ASN][1000 genomes]
rs62170864	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170865	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62170866	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62170872	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62170895	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62170896	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62170899	0.90[EUR][1000 genomes]
rs62170910	0.83[EUR][1000 genomes]
rs62170911	0.83[EUR][1000 genomes]
rs62170914	0.83[EUR][1000 genomes]
rs62170916	0.83[EUR][1000 genomes]
rs62170918	0.81[EUR][1000 genomes]
rs62171961	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62171964	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62171994	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62171995	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62171996	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62171997	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66769122	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715833	0.84[CHB][hapmap]
rs6742824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823135	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823137	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823174	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823176	0.93[EUR][1000 genomes]
rs72823182	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823183	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823195	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72823196	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72823197	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72825338	0.80[EUR][1000 genomes]
rs7570003	0.82[TSI][hapmap]
rs956657	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9808165	0.86[LWK][hapmap]

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	esv2752990	chr2:77038541-77217310	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv834266	chr2:77120236-77287504	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv519950	chr2:77213103-77256291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13388459	FAM176A	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77214000-77220400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:77214200-77217400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:77215400-77215800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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