Variant report

Variant	rs1486234
Chromosome Location	chr2:180707742-180707743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:180697026..180699896-chr2:180705650..180708149,2	MCF-7	breast:
2	chr2:180707046..180707794-chr2:180801109..180802085,4	MCF-7	breast:
3	chr2:180706168..180708341-chr2:180711093..180713264,3	K562	blood:
4	chr2:180707129..180707861-chr2:180763387..180764295,2	K562	blood:
5	chr2:180706972..180707878-chr2:180763320..180764150,2	MCF-7	breast:
6	chr2:180706968..180707872-chr2:180831565..180832499,2	MCF-7	breast:
7	chr2:180707163..180707821-chr2:180941894..180942731,3	MCF-7	breast:
8	chr2:180707295..180707909-chr2:180763473..180764251,2	MCF-7	breast:

No data

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10183495	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.84[EUR][1000 genomes]
rs10185471	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195952	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205122	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13388545	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398994	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs13399189	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs13399303	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13407401	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13410767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs13418648	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1351416	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352110	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480705	0.96[ASN][1000 genomes]
rs1480706	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480707	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867014	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs4894128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894129	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894130	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6706312	1.00[CHB][hapmap]
rs7570985	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes]
rs7573137	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs7588510	0.84[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs7601013	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7603617	0.94[ASW][hapmap];0.96[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607354	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs966440	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[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	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
rs1486234	HOXD13	cis	cerebellum	SCAN

Chromatin state (count:4 , 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
2	chr2:180707200-180707800	Enhancers	Liver	Liver
3	chr2:180707400-180707800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr2:180707400-180707800	Enhancers	Fetal Lung	lung

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