Variant report

Variant	rs11111555
Chromosome Location	chr12:103800959-103800960
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:103799013..103801250-chr12:103801844..103804662,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10161272	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10507166	0.83[CEU][hapmap];0.87[CHB][hapmap]
rs10745962	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs10745963	0.81[ASN][1000 genomes]
rs10745964	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10745965	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778240	0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10778241	0.83[ASW][hapmap];0.91[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778246	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10778253	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs10778257	0.86[CHB][hapmap]
rs10860997	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10861000	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861005	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10861013	0.95[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10861015	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10861016	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111551	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11111556	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11111572	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11111579	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11111582	0.86[EUR][1000 genomes]
rs1320345	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2374045	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374056	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2374057	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2374062	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs2374065	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2374078	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2888733	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6539073	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295887	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298211	0.91[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7300757	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7301460	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7302890	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7303147	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7304308	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7305704	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs7312095	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313836	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313920	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7952759	0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7961410	0.86[CHB][hapmap]
rs7967003	0.87[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7967288	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7970043	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7970506	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455703	chr12:103692799-103818049	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv560037	chr12:103692799-103818049	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899477	chr12:103747515-103817326	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv899478	chr12:103747515-103834275	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11111555	FAM71C	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103795200-103801600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:103795200-103814000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:103799000-103802800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:103799600-103801600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:103799600-103801800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:103799600-103803000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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