Variant report

Variant	rs12328338
Chromosome Location	chr2:180712985-180712986
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	chr2:180711911..180714659-chr2:180717451..180719062,2	MCF-7	breast:
2	chr2:180706168..180708341-chr2:180711093..180713264,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10183495	0.83[CEU][hapmap]
rs10185471	0.83[CEU][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs10195952	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs10930887	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs12053220	0.90[JPT][hapmap]
rs12053223	0.90[JPT][hapmap]
rs12053553	0.90[JPT][hapmap]
rs12465175	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13407401	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs1351416	0.83[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs1383413	0.81[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs1480706	0.85[TSI][hapmap]
rs1480707	0.83[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs1486233	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165379	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs165380	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs165381	0.86[ASN][1000 genomes]
rs16867045	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs187745	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1906012	0.92[CEU][hapmap]
rs194674	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs2170240	0.85[ASN][1000 genomes]
rs2219670	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2367797	0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs259831	0.97[ASN][1000 genomes]
rs259833	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs259845	0.80[EUR][1000 genomes]
rs259849	0.80[ASN][1000 genomes]
rs2630539	0.96[ASN][1000 genomes]
rs357714	0.85[CHD][hapmap];0.80[MEX][hapmap]
rs55869281	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56152328	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56388438	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6433810	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6433811	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6750809	0.80[EUR][1000 genomes]
rs6752731	0.80[MEX][hapmap]
rs7557122	0.80[MEX][hapmap]
rs7570985	0.88[CEU][hapmap]
rs7573137	0.83[CEU][hapmap]
rs7585592	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7588510	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7597666	0.80[MEX][hapmap]
rs7607354	0.88[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][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	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428731	chr2:180629389-180805171	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv875472	chr2:180696414-181024926	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv875473	chr2:180696414-181055597	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12328338	HOXD13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180706800-180724800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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