Variant report

Variant	rs13160133
Chromosome Location	chr5:43225634-43225635
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43121173..43123733-chr5:43225214..43227134,2	MCF-7	breast:
2	chr5:43120976..43123140-chr5:43225337..43226938,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGCS1-2	chr5:43225608-43225915	NONHSAT101302

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001717	0.82[CEU][hapmap]
rs1084520	1.00[ASN][1000 genomes]
rs13154319	1.00[CHB][hapmap]
rs13155023	1.00[CHB][hapmap]
rs13158147	1.00[ASN][1000 genomes]
rs13163892	0.80[CEU][hapmap]
rs13164183	0.80[CEU][hapmap]
rs13164889	0.89[CEU][hapmap]
rs13167375	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13167991	1.00[ASN][1000 genomes]
rs13169195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13170959	1.00[ASN][1000 genomes]
rs13171192	1.00[ASN][1000 genomes]
rs13175754	1.00[ASN][1000 genomes]
rs13180496	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13180902	1.00[CHB][hapmap]
rs13186091	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13186549	1.00[CEU][hapmap]
rs17242731	0.82[CEU][hapmap]
rs17242995	0.90[CEU][hapmap]
rs17303482	0.80[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085100	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34157680	1.00[ASN][1000 genomes]
rs34517361	1.00[ASN][1000 genomes]
rs34735159	1.00[ASN][1000 genomes]
rs34810824	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35397154	0.80[CEU][hapmap]
rs35756781	1.00[ASN][1000 genomes]
rs35764948	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752831	0.80[CEU][hapmap]
rs3752832	0.82[CEU][hapmap]
rs505573	1.00[ASN][1000 genomes]
rs614386	1.00[ASN][1000 genomes]
rs632730	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71627588	0.84[EUR][1000 genomes]
rs71627590	0.82[EUR][1000 genomes]
rs71627591	0.84[EUR][1000 genomes]
rs71627592	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71627594	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs878234	0.80[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43196200-43245400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:43209600-43245200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:43215600-43236800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:43219000-43226000	Weak transcription	Brain Angular Gyrus	brain
5	chr5:43219200-43232000	Weak transcription	Brain Anterior Caudate	brain
6	chr5:43225200-43226600	Enhancers	Thymus	Thymus
7	chr5:43225600-43226400	Enhancers	Stomach Mucosa	stomach
8	chr5:43225600-43228200	Enhancers	K562	blood

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