Variant report

Variant	rs4575469
Chromosome Location	chr14:77860543-77860544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77859431..77861552-chr14:77871084..77872888,2	K562	blood:
2	chr14:77859416..77861552-chr14:77870946..77872888,2	K562	blood:
3	chr14:77837819..77844743-chr14:77858917..77867107,14	MCF-7	breast:
4	chr14:77851627..77854114-chr14:77860250..77862122,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100580	Chromatin interaction
ENSG00000100583	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10133896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061629	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1061638	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11159258	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11159259	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11159261	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs11159262	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11159263	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11159264	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11622359	0.89[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap]
rs11623826	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11624990	0.85[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs11625365	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11627016	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11844594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12101153	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12432247	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12433766	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs12435136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12436593	0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs12587525	0.81[CEU][hapmap]
rs12885869	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12889722	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13379432	0.87[CHD][hapmap]
rs147316	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs176766	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176767	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs176768	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176772	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs176773	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs176778	0.82[EUR][1000 genomes]
rs176781	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17824034	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17824214	0.85[CHD][hapmap]
rs17824316	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap]
rs2063997	0.87[CHD][hapmap]
rs2091916	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2193595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2242619	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2364156	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35881785	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4223	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4369582	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4899652	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4899654	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899655	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4903576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4903577	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4903579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4903580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4903584	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs4903586	0.89[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap]
rs6574372	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66466131	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7142380	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs7146595	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs7146784	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs7150718	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7155063	0.87[CHD][hapmap]
rs7250	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap]
rs8005759	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8006688	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8016070	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8016576	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8017215	0.87[CHD][hapmap]
rs8018513	0.80[EUR][1000 genomes]
rs8018711	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8018808	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963283	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.87[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	nsv902107	chr14:77790416-77871777	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1362	chr14:77853202-77898605	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4575469	C14orf148	cis	cerebellum	SCAN
rs4575469	C14orf148	cis	parietal	SCAN
rs4575469	C14orf174	cis	parietal	SCAN
rs4575469	AHSA1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77844400-77862200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:77856200-77860800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:77858800-77862000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:77859600-77886200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr14:77860000-77872400	Weak transcription	Brain Anterior Caudate	brain

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