Variant report

Variant	rs10898215
Chromosome Location	chr11:83942165-83942166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:83941713..83944829-chr11:83950244..83953336,4	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10128587	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs1022308	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.97[ASN][1000 genomes]
rs1040131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10751105	0.88[ASW][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs10751106	0.89[JPT][hapmap]
rs10751109	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10751112	0.98[ASN][1000 genomes]
rs10792727	0.83[JPT][hapmap]
rs10792731	0.83[CHD][hapmap];0.88[JPT][hapmap]
rs10792740	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs10792742	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs10792744	0.91[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10792745	0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10792746	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10898214	0.90[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs10898216	0.99[ASN][1000 genomes]
rs10898217	0.98[ASN][1000 genomes]
rs10898218	0.98[ASN][1000 genomes]
rs10898219	0.97[ASN][1000 genomes]
rs10898222	0.95[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11233953	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs11233954	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs11233956	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs11233963	0.85[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11233967	0.91[CHB][hapmap];0.91[ASN][1000 genomes]
rs12278134	0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12281587	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs1349820	0.89[JPT][hapmap]
rs1377746	0.83[JPT][hapmap]
rs1377747	0.83[JPT][hapmap]
rs1377748	0.89[JPT][hapmap]
rs1399617	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.97[ASN][1000 genomes]
rs1399618	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs1454021	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.99[ASN][1000 genomes]
rs1454023	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs1454026	0.89[JPT][hapmap]
rs1515084	0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs1515091	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1515092	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs1515094	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1573572	0.83[JPT][hapmap]
rs1793037	0.83[JPT][hapmap]
rs1849877	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs1869470	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.84[YRI][hapmap];0.99[ASN][1000 genomes]
rs1869471	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs1869472	0.83[JPT][hapmap]
rs1901973	0.98[ASN][1000 genomes]
rs2156848	0.89[JPT][hapmap]
rs2374526	0.97[ASN][1000 genomes]
rs4354715	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.97[ASN][1000 genomes]
rs4943889	0.91[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4944471	0.89[JPT][hapmap]
rs4944472	0.89[JPT][hapmap]
rs4944474	0.98[ASN][1000 genomes]
rs7103429	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7106175	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7112322	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7122248	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7130225	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs73519747	0.99[ASN][1000 genomes]
rs7483548	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs7925243	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7933566	0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs7937925	0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7941004	0.89[JPT][hapmap]
rs7943267	0.83[JPT][hapmap]
rs896996	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs896997	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs896998	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs930790	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs963259	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[ASN][1000 genomes]
rs988322	0.83[JPT][hapmap]

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	nsv1039924	chr11:83662904-83993497	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv541102	chr11:83662904-83993497	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv948410	chr11:83918339-84812001	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv415	chr11:83924941-83969603	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10898215	FZD4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:83935200-83945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:83935400-83944600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:83936600-83942400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:83939600-83945200	Weak transcription	Brain Germinal Matrix	brain
5	chr11:83940000-83943600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:83940000-83944000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:83940000-83945000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:83940600-83944200	Weak transcription	Brain Anterior Caudate	brain
9	chr11:83940800-83945000	Weak transcription	Brain Angular Gyrus	brain
10	chr11:83941000-83946200	Enhancers	Brain Hippocampus Middle	brain

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