Variant report

Variant	rs12568612
Chromosome Location	chr1:223879083-223879084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223877159..223879114-chr1:224033630..224035286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10465524	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs10495215	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs10495216	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10495217	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10503144	0.85[CEU][hapmap]
rs10799550	0.91[EUR][1000 genomes]
rs10916600	0.80[EUR][1000 genomes]
rs10916601	0.81[EUR][1000 genomes]
rs10916602	0.81[EUR][1000 genomes]
rs10916603	0.80[EUR][1000 genomes]
rs10916634	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs10916646	0.87[CEU][hapmap]
rs12059770	0.85[CEU][hapmap]
rs12070364	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs12074091	0.81[EUR][1000 genomes]
rs12080250	0.85[CEU][hapmap]
rs12088254	0.85[CEU][hapmap]
rs12563637	0.85[CEU][hapmap]
rs12565967	0.85[CEU][hapmap]
rs12566817	0.85[CEU][hapmap]
rs12567519	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419305	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs1629836	0.82[CEU][hapmap]
rs16842162	0.85[CEU][hapmap]
rs16842257	0.85[CEU][hapmap]
rs16842326	0.85[CEU][hapmap]
rs17556570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557288	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17557525	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17557623	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1779658	0.87[CEU][hapmap]
rs1892076	0.80[EUR][1000 genomes]
rs1892077	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs1936525	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2186006	0.87[CEU][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs28370014	0.80[EUR][1000 genomes]
rs28739569	0.81[EUR][1000 genomes]
rs41307690	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4511081	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653499	0.81[EUR][1000 genomes]
rs4653500	0.80[EUR][1000 genomes]
rs4653522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59990581	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61450747	0.83[EUR][1000 genomes]
rs61822582	0.92[EUR][1000 genomes]
rs61822583	0.93[EUR][1000 genomes]
rs61822586	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822630	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822631	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822632	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822633	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822634	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822635	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61822636	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823962	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823965	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61823966	0.81[EUR][1000 genomes]
rs61823967	0.83[EUR][1000 genomes]
rs61823968	0.83[EUR][1000 genomes]
rs61825227	0.84[EUR][1000 genomes]
rs6604724	0.85[CEU][hapmap]
rs6656416	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669046	0.87[CEU][hapmap]
rs6671245	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6678365	0.85[CEU][hapmap]
rs6683052	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs6685475	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6685557	0.85[CEU][hapmap]
rs6690568	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691315	0.85[CEU][hapmap]
rs6693372	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs6693884	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6694960	0.85[CEU][hapmap]
rs6696053	0.85[CEU][hapmap]
rs6700366	0.85[CEU][hapmap]
rs6702314	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6702430	0.93[EUR][1000 genomes]
rs6703104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7331	0.85[CEU][hapmap]
rs7412088	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs7414311	0.81[EUR][1000 genomes]
rs7530328	0.85[CEU][hapmap]
rs7533551	0.85[CEU][hapmap]
rs7535882	0.85[CEU][hapmap]
rs7543197	0.86[CEU][hapmap]
rs7547642	0.87[CEU][hapmap]
rs7549063	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs7551783	0.82[YRI][hapmap];0.96[EUR][1000 genomes]
rs7555491	0.87[CEU][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12568612	MARK1	cis	parietal	SCAN
rs12568612	CAPN2	Cis_1M	lymphoblastoid	RTeQTL
rs12568612	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223876400-223885600	Weak transcription	A549	lung
2	chr1:223878800-223884000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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