Variant report

Variant	rs4775817
Chromosome Location	chr15:49960752-49960753
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49955894..49958426-chr15:49959044..49961456,2	MCF-7	breast:
2	chr15:49959156..49961709-chr15:49969639..49971323,2	MCF-7	breast:
3	chr15:49912031..49914987-chr15:49959413..49961383,3	MCF-7	breast:
4	chr15:49958418..49961661-chr15:49962347..49965829,3	K562	blood:

Variant related genes	Relation type
ENSG00000104047	Chromatin interaction
ENSG00000166262	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10047970	0.81[EUR][1000 genomes]
rs10083602	0.83[EUR][1000 genomes]
rs10152754	0.82[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10152787	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10162802	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10467920	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1048348	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1057636	0.82[EUR][1000 genomes]
rs1057638	0.84[EUR][1000 genomes]
rs11070694	0.83[EUR][1000 genomes]
rs11070696	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070708	0.81[EUR][1000 genomes]
rs11070713	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11630629	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11631904	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11632003	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11634751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11636378	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11857320	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12185128	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12437460	0.84[EUR][1000 genomes]
rs12437899	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438444	0.84[EUR][1000 genomes]
rs12438856	0.83[EUR][1000 genomes]
rs12440099	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440323	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12441004	0.82[EUR][1000 genomes]
rs12441304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12442143	0.83[EUR][1000 genomes]
rs12443123	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905627	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1395902	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1532955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs1588130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1588131	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1588132	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs1605477	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1605478	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1605479	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1605481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1605484	0.82[EUR][1000 genomes]
rs16962528	0.83[EUR][1000 genomes]
rs16973952	0.83[EUR][1000 genomes]
rs17401417	0.83[EUR][1000 genomes]
rs17482113	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848289	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1857992	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1874612	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1874615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs1911614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2007474	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2413946	0.83[EUR][1000 genomes]
rs2413953	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413957	0.81[EUR][1000 genomes]
rs2413959	0.81[EUR][1000 genomes]
rs2601020	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28460471	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28562087	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28788326	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28815194	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28822970	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28836194	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28841970	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28842346	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28871940	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2899433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2899448	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4303431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4321137	0.82[EUR][1000 genomes]
rs4350524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs4614670	0.83[EUR][1000 genomes]
rs4775811	0.84[EUR][1000 genomes]
rs4775814	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs4775815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs553439	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55993510	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56094557	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56335122	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56692783	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs57186766	0.82[EUR][1000 genomes]
rs57421305	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57980364	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57997677	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58284238	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58410445	0.83[EUR][1000 genomes]
rs60728602	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62009983	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62009985	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62021583	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62021584	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62021585	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62021586	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62021587	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493371	0.83[EUR][1000 genomes]
rs6493373	0.84[EUR][1000 genomes]
rs6493376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67428220	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67916122	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68095295	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs692008	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7162351	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162792	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162800	1.00[CHB][hapmap];0.87[MEX][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7166049	0.83[EUR][1000 genomes]
rs7166202	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7166498	0.83[EUR][1000 genomes]
rs7167041	0.83[EUR][1000 genomes]
rs7167429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7168031	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7170426	0.83[EUR][1000 genomes]
rs7176350	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7177247	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7178143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs7178194	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7178468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7181916	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7182072	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7183313	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs731051	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs733097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8026236	0.83[EUR][1000 genomes]
rs8027730	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs8029561	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8029743	0.86[EUR][1000 genomes]
rs8030761	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8034202	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8035468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036139	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8039062	0.84[EUR][1000 genomes]
rs8041493	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs906419	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs925103	0.82[EUR][1000 genomes]
rs9302148	0.83[EUR][1000 genomes]
rs962710	0.82[EUR][1000 genomes]
rs9635335	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs965134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9972329	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9972429	0.83[EUR][1000 genomes]
rs9972565	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4775817	CATSPER2P1	cis	cerebellum	SCAN
rs4775817	DTWD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49955600-49961400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:49956600-49961400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:49957200-49965600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:49960400-49965400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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