Variant report

Variant	rs17767398
Chromosome Location	chr14:71770485-71770486
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71768291..71772700-chr14:71783468..71788933,6	MCF-7	breast:
2	chr14:71767096..71772420-chr14:71785571..71789384,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259146	Chromatin interaction
ENSG00000197555	Chromatin interaction

Extended variants
information (count: 155 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs11620632	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11627918	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs11845249	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs11849508	0.84[ASN][1000 genomes]
rs12127	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12878989	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879243	0.83[EUR][1000 genomes]
rs12880291	0.91[EUR][1000 genomes]
rs12880611	0.83[EUR][1000 genomes]
rs12881643	0.86[EUR][1000 genomes]
rs12881957	0.86[EUR][1000 genomes]
rs12884929	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12887261	0.91[EUR][1000 genomes]
rs12889866	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12891975	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12894016	0.83[EUR][1000 genomes]
rs12894478	0.86[EUR][1000 genomes]
rs12896900	0.82[EUR][1000 genomes]
rs12896986	0.83[EUR][1000 genomes]
rs14030	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17178045	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17178206	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs17178234	0.83[EUR][1000 genomes]
rs17178387	0.82[EUR][1000 genomes]
rs17767362	0.81[AMR][1000 genomes]
rs17767380	0.82[EUR][1000 genomes]
rs17767386	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17767392	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767410	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17767446	0.87[EUR][1000 genomes]
rs17767499	0.86[EUR][1000 genomes]
rs17767523	0.83[EUR][1000 genomes]
rs17767553	0.87[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1990241	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2108049	0.83[EUR][1000 genomes]
rs2108706	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2108707	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2109276	0.83[EUR][1000 genomes]
rs2159145	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286409	0.92[ASW][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap]
rs2877729	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs33994051	0.83[EUR][1000 genomes]
rs34011442	0.90[EUR][1000 genomes]
rs34057981	0.83[EUR][1000 genomes]
rs34061264	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34176710	0.82[EUR][1000 genomes]
rs34281405	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34281934	0.84[EUR][1000 genomes]
rs34320622	0.83[EUR][1000 genomes]
rs34347034	0.83[EUR][1000 genomes]
rs34388001	0.91[EUR][1000 genomes]
rs34454371	0.83[EUR][1000 genomes]
rs34469007	0.83[EUR][1000 genomes]
rs34524083	0.87[EUR][1000 genomes]
rs34528013	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34528131	0.87[EUR][1000 genomes]
rs34533948	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34649709	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34674149	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34725136	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34746156	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34748537	0.87[EUR][1000 genomes]
rs34767050	0.92[EUR][1000 genomes]
rs34873919	0.89[EUR][1000 genomes]
rs34911660	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34957192	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34991781	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34993988	0.86[EUR][1000 genomes]
rs35051046	0.86[EUR][1000 genomes]
rs35054229	0.91[EUR][1000 genomes]
rs35094946	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35122644	0.90[EUR][1000 genomes]
rs35151594	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35260692	0.87[EUR][1000 genomes]
rs35468256	0.86[EUR][1000 genomes]
rs35589413	0.81[EUR][1000 genomes]
rs35609708	0.82[EUR][1000 genomes]
rs35613269	0.83[EUR][1000 genomes]
rs35620527	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35621718	0.90[EUR][1000 genomes]
rs35625243	0.90[EUR][1000 genomes]
rs35680546	0.82[EUR][1000 genomes]
rs35692397	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35796129	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35822724	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35831373	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35854505	0.86[EUR][1000 genomes]
rs35866366	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36052007	0.82[EUR][1000 genomes]
rs36057816	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36093218	0.85[EUR][1000 genomes]
rs4453405	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4902928	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55863348	0.81[AMR][1000 genomes]
rs56201715	0.80[ASN][1000 genomes]
rs56363446	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56407721	0.86[EUR][1000 genomes]
rs59697713	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61989245	0.84[ASN][1000 genomes]
rs61989246	0.84[ASN][1000 genomes]
rs61989247	0.84[ASN][1000 genomes]
rs61989250	0.84[ASN][1000 genomes]
rs61989252	0.81[AMR][1000 genomes]
rs61989255	0.81[AMR][1000 genomes]
rs61989256	0.81[AMR][1000 genomes]
rs61989257	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61989367	0.83[EUR][1000 genomes]
rs61989373	0.83[EUR][1000 genomes]
rs61989374	0.83[EUR][1000 genomes]
rs61989377	0.83[EUR][1000 genomes]
rs61989379	0.91[EUR][1000 genomes]
rs61989382	0.82[EUR][1000 genomes]
rs61989386	0.82[EUR][1000 genomes]
rs61991192	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61991195	0.82[EUR][1000 genomes]
rs61991199	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61991200	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61991201	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61991202	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61991203	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61991204	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61991205	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61991213	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61991243	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61991246	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61991247	0.87[EUR][1000 genomes]
rs61991248	0.87[EUR][1000 genomes]
rs61991249	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61991250	0.85[EUR][1000 genomes]
rs61991255	0.83[EUR][1000 genomes]
rs66645707	0.82[EUR][1000 genomes]
rs67489015	0.86[EUR][1000 genomes]
rs68073803	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7140354	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7142180	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7142214	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145755	0.86[EUR][1000 genomes]
rs7147434	0.88[EUR][1000 genomes]
rs7147668	0.87[EUR][1000 genomes]
rs7152842	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7156460	0.87[EUR][1000 genomes]
rs7160460	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs722633	0.83[EUR][1000 genomes]
rs723966	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs725673	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs72726701	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72726702	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72728403	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72728427	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8007068	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8015644	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8019721	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17767398	PCNX	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71758600-71772800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:71762400-71771400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr14:71763200-71771400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:71770200-71771200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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