Variant report

Variant	rs12916123
Chromosome Location	chr15:74638965-74638966
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74632720..74634686-chr15:74636521..74639007,2	MCF-7	breast:
2	chr15:74606974..74610112-chr15:74636759..74639139,3	K562	blood:
3	chr15:74638641..74640851-chr15:74642366..74644922,2	K562	blood:
4	chr15:74635843..74637351-chr15:74638893..74640725,2	MCF-7	breast:
5	chr15:74628941..74630782-chr15:74637819..74639455,2	K562	blood:
6	chr15:74607938..74610112-chr15:74637389..74639139,2	K562	blood:

Variant related genes	Relation type
ENSG00000260266	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11072478	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs11072479	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898858	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913682	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12914852	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1484216	0.84[CEU][hapmap]
rs1564782	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs16968477	0.89[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1843090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][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]
rs1843091	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2277601	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2277602	0.96[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2277605	0.83[EUR][1000 genomes]
rs2277606	0.88[EUR][1000 genomes]
rs2279356	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2279357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2415239	0.80[EUR][1000 genomes]
rs2930300	0.84[CEU][hapmap]
rs2930302	0.84[CEU][hapmap]
rs2930304	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2930305	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2930306	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs2959002	0.95[EUR][1000 genomes]
rs2959004	0.96[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2959006	0.84[CEU][hapmap]
rs2959007	0.84[CEU][hapmap]
rs2959008	0.84[CEU][hapmap]
rs4077581	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4077582	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs41556118	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174179	1.00[ASW][hapmap];1.00[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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031121	0.81[CEU][hapmap]
rs8031424	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs900802	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[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	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv904351	chr15:74638965-74697084	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12916123	C15orf39	cis	cerebellum	SCAN
rs12916123	C15orf28	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74612000-74657800	Weak transcription	Right Atrium	heart
2	chr15:74628000-74642200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr15:74638000-74640000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:74638000-74642800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:74638200-74642800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:74638600-74641400	Strong transcription	Placenta	Placenta

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