Variant report

Variant	rs1879621
Chromosome Location	chr12:103748475-103748476
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:103745859..103749136-chr12:103750822..103754295,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10778228	0.95[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10778231	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10778232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10778236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10778237	0.95[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10778238	0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10860977	0.95[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs10860989	0.86[CEU][hapmap]
rs10860990	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11111537	0.86[CEU][hapmap]
rs11111540	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12301542	0.90[CEU][hapmap]
rs12305336	0.86[CEU][hapmap]
rs1343868	0.94[EUR][1000 genomes]
rs1996749	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2374052	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2374060	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2374061	0.91[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4764732	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4764733	0.86[CEU][hapmap]
rs4764949	0.86[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs4764952	0.89[EUR][1000 genomes]
rs4764955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539066	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6539069	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539070	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539071	0.85[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7137989	0.95[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs7316140	0.81[CEU][hapmap]
rs7969597	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7970479	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970531	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7971321	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8181626	0.96[EUR][1000 genomes];0.87[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
rs1879621	EID3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103707200-103786400	Weak transcription	Primary B cells from cord blood	blood
2	chr12:103745600-103755800	Weak transcription	Spleen	Spleen
3	chr12:103745800-103750000	Strong transcription	Primary B cells from peripheral blood	blood
4	chr12:103747200-103763400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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