Variant report

Variant	rs7651972
Chromosome Location	chr3:70114499-70114500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1027233	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1027234	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1157456	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12495230	0.80[MEX][hapmap]
rs1491686	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1491694	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[ASN][1000 genomes]
rs1491696	0.87[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1491697	0.85[ASN][1000 genomes]
rs1491700	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1492055	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1492056	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17729465	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17729489	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17785152	0.91[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.80[ASN][1000 genomes]
rs17785756	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2101636	0.86[ASN][1000 genomes]
rs2131122	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2874269	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855334	0.88[ASN][1000 genomes]
rs4855335	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60403843	0.82[ASN][1000 genomes]
rs60647884	0.80[ASN][1000 genomes]
rs61645126	0.84[ASN][1000 genomes]
rs6549266	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6549267	0.92[ASN][1000 genomes]
rs6763730	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6799525	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7611660	0.82[ASW][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[LWK][hapmap];0.90[YRI][hapmap]
rs7619924	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7634340	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7634564	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7645353	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7647661	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7649560	1.00[YRI][hapmap]
rs9310181	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9815027	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9818964	0.87[AFR][1000 genomes]
rs9837453	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9840951	0.87[ASN][1000 genomes]
rs9856462	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7651972	RP11-460N16.1	cis	Artery Aorta	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70107400-70116800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:70107400-70120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:70107600-70120200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:70112600-70115200	Enhancers	Fetal Brain Male	brain
5	chr3:70112600-70120600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:70112800-70115000	Enhancers	Brain Hippocampus Middle	brain
7	chr3:70113000-70117600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:70113200-70114800	Enhancers	Brain Angular Gyrus	brain
9	chr3:70113200-70115000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:70113800-70119800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:70113800-70120200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:70113800-70120400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:70113800-70120400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:70113800-70123800	Weak transcription	Gastric	stomach
15	chr3:70114000-70114800	Weak transcription	Aorta	Aorta
16	chr3:70114000-70117000	Weak transcription	Psoas Muscle	Psoas

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