Variant report

Variant	rs11168514
Chromosome Location	chr12:48699276-48699277
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	chr12:48698712..48702509-chr12:48702715..48705745,3	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10082861	0.85[JPT][hapmap]
rs1021313	0.93[ASN][1000 genomes]
rs10219623	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs10431526	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10437919	0.93[ASN][1000 genomes]
rs10437920	0.93[ASN][1000 genomes]
rs10467101	0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875745	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10875746	0.87[JPT][hapmap]
rs10875750	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10875767	0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10875768	0.87[ASN][1000 genomes]
rs10875769	0.82[ASN][1000 genomes]
rs10875770	0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs10875772	0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.91[ASN][1000 genomes]
rs10875777	0.93[ASN][1000 genomes]
rs10875778	0.93[ASN][1000 genomes]
rs10875779	0.93[ASN][1000 genomes]
rs10875782	0.90[ASN][1000 genomes]
rs10875792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875799	0.87[ASN][1000 genomes]
rs11168413	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168414	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168418	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168420	0.87[JPT][hapmap]
rs11168421	0.87[JPT][hapmap]
rs11168425	0.87[JPT][hapmap]
rs11168427	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168433	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11168450	0.87[JPT][hapmap]
rs11168459	0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs11168483	0.90[ASN][1000 genomes]
rs11168487	0.93[ASN][1000 genomes]
rs11168493	0.95[ASN][1000 genomes]
rs11168508	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168510	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168520	0.86[ASN][1000 genomes]
rs11168536	0.87[ASN][1000 genomes]
rs12227601	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12297470	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12300647	0.90[ASN][1000 genomes]
rs12305511	0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs12305647	0.82[ASN][1000 genomes]
rs12310813	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs12312134	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12313745	0.85[ASN][1000 genomes]
rs12317751	0.93[ASN][1000 genomes]
rs12318705	0.90[ASN][1000 genomes]
rs12322347	0.85[ASN][1000 genomes]
rs12322348	0.85[ASN][1000 genomes]
rs1471997	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs17122666	0.87[JPT][hapmap]
rs17122812	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1859445	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs2012773	0.87[JPT][hapmap]
rs2054903	0.94[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2054904	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107638	0.87[JPT][hapmap]
rs2171642	0.90[ASN][1000 genomes]
rs2228500	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2269933	0.87[JPT][hapmap]
rs2269935	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2279464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2409005	0.87[ASN][1000 genomes]
rs2450992	0.81[ASN][1000 genomes]
rs2634675	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2732439	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2732465	0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2898065	0.92[ASN][1000 genomes]
rs2898066	0.88[ASN][1000 genomes]
rs3185921	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs3751273	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs4760619	0.90[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap]
rs4760622	0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4760625	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760681	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4760687	0.87[JPT][hapmap]
rs4760695	0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4760696	0.87[JPT][hapmap]
rs4760697	0.87[JPT][hapmap]
rs4760699	0.86[ASN][1000 genomes]
rs61940962	0.89[ASN][1000 genomes]
rs61941003	0.93[ASN][1000 genomes]
rs61941006	0.93[ASN][1000 genomes]
rs6580659	0.85[JPT][hapmap]
rs7135779	0.85[JPT][hapmap]
rs716553	0.93[ASN][1000 genomes]
rs725454	0.87[JPT][hapmap]
rs7297298	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302466	0.90[ASN][1000 genomes]
rs7303055	0.93[ASN][1000 genomes]
rs7486008	0.93[ASN][1000 genomes]
rs7486424	0.87[JPT][hapmap]
rs7975956	0.90[ASN][1000 genomes]
rs8804	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs9634261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899062	chr12:48658212-48711867	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv899063	chr12:48664989-48713768	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv899065	chr12:48667019-48711867	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv899066	chr12:48667019-48713768	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	esv34952	chr12:48672333-48703533	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv469369	chr12:48675783-48711867	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv469370	chr12:48675783-48711867	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv469372	chr12:48675783-48711867	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv470290	chr12:48675783-48711867	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv558791	chr12:48675783-48711867	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11168514	RP1-228P16.1	cis	Thyroid	GTEx
rs11168514	FAM186B	cis	parietal	SCAN
rs11168514	H1FNT	cis	cerebellum	SCAN
rs11168514	ARID2	cis	parietal	SCAN
rs11168514	ZNF641	cis	cerebellum	SCAN
rs11168514	RND1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48699200-48699800	Enhancers	Fetal Heart	heart

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