Variant report

Variant	rs1996661
Chromosome Location	chr14:72795361-72795362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72794559..72797059-chr14:72803417..72805844,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10146126	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10149207	0.86[YRI][hapmap]
rs11620677	0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs1356842	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1402063	0.93[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1402064	0.93[CHB][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2090736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2139596	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs2190509	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2222311	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2238195	0.88[ASW][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs2238204	0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs2238206	0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2238207	0.85[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs2239244	0.81[AMR][1000 genomes]
rs2239246	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[LWK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2250557	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2250666	0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2529459	0.83[CEU][hapmap]
rs2529474	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2529476	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2681724	0.86[EUR][1000 genomes]
rs2681729	0.84[AMR][1000 genomes]
rs2681732	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2681739	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2681740	0.84[AMR][1000 genomes]
rs2681750	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2681770	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4899430	0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs6574061	0.80[AMR][1000 genomes]
rs6574065	0.82[AMR][1000 genomes]
rs699366	0.89[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7151952	0.96[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs765221	0.94[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs847331	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs847334	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs847346	0.93[GIH][hapmap];0.89[JPT][hapmap]
rs847348	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs847349	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs847350	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs847360	0.84[CHD][hapmap]
rs847362	0.85[CHD][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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1996661	TTC9	cis	parietal	SCAN
rs1996661	TMED10	cis	parietal	SCAN
rs1996661	PI16	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72794400-72798200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr14:72794600-72797800	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:72795200-72796600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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