Variant report

Variant	rs12111645
Chromosome Location	chr7:120212069-120212070
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	chr7:120204677..120206283-chr7:120210805..120213588,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10085583	1.00[ASN][1000 genomes]
rs10156125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227379	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[EUR][1000 genomes]
rs10228326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10234674	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10239065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10242908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10243095	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10245675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247657	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10248007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259436	1.00[EUR][1000 genomes]
rs10261574	1.00[ASN][1000 genomes]
rs10262476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268591	1.00[CHD][hapmap]
rs10270560	1.00[CEU][hapmap];1.00[CHB][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]
rs10270911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10272979	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10273127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10273242	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10277086	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10282150	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10488302	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[EUR][1000 genomes]
rs11536582	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12111791	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171571	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13438753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527650	1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs1527654	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1609181	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[EUR][1000 genomes]
rs16870516	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17142782	1.00[CHD][hapmap]
rs17142844	1.00[EUR][1000 genomes]
rs17142852	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17142856	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17142860	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17283053	1.00[EUR][1000 genomes]
rs17347436	1.00[EUR][1000 genomes]
rs17355253	1.00[EUR][1000 genomes]
rs2049643	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454884	0.95[EUR][1000 genomes]
rs4540347	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs60967957	1.00[EUR][1000 genomes]
rs6466749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970111	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs73441852	1.00[EUR][1000 genomes]
rs7357256	1.00[CEU][hapmap];1.00[CHB][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]
rs7808927	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9640793	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9641643	1.00[CHB][hapmap]
rs9641644	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9641645	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9886093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv516686	chr7:120015843-120223084	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv889117	chr7:120122040-120266458	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12111645	KCND2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120200400-120223000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr7:120211400-120212200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:120211600-120212200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:120211600-120212400	Enhancers	Cortex derived primary cultured neurospheres	brain

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