Variant report

Variant	rs1732396
Chromosome Location	chr12:121363598-121363599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121362910..121365338-chr12:121366492..121368266,2	K562	blood:
2	chr12:121358068..121359708-chr12:121361498..121363988,2	MCF-7	breast:
3	chr12:121341649..121345411-chr12:121362011..121364307,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1067742	0.84[EUR][1000 genomes]
rs10774577	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849818	0.88[ASN][1000 genomes]
rs1105416	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1151850	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1151851	0.86[ASN][1000 genomes]
rs1151852	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1151861	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1151863	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1151864	0.80[ASN][1000 genomes]
rs1168945	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1168954	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1168956	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1696361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1696363	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1718209	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1718211	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732398	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732405	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2454729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649994	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2649995	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2649996	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2649998	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650006	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2701174	0.80[ASN][1000 genomes]
rs2701178	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2701181	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2701182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491602	0.87[EUR][1000 genomes]
rs538785	0.86[EUR][1000 genomes]
rs618849	0.85[EUR][1000 genomes]
rs628771	0.87[EUR][1000 genomes]
rs631168	0.86[EUR][1000 genomes]
rs683091	0.87[EUR][1000 genomes]
rs688402	0.87[EUR][1000 genomes]
rs7300722	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791713	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv560448	chr12:121341477-121364324	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv560453	chr12:121342186-121364324	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1838192	chr12:121363589-121402932	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1732396	SPPL3	cis	Adipose Subcutaneous	GTEx
rs1732396	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121362800-121363800	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr12:121362800-121363800	Enhancers	HMEC	breast
3	chr12:121362800-121364400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr12:121362800-121364400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:121362800-121364400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:121362800-121364400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:121362800-121364400	Enhancers	Placenta	Placenta
8	chr12:121362800-121364600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:121362800-121364600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:121363000-121363600	Enhancers	Fetal Thymus	thymus
11	chr12:121363000-121363600	Enhancers	NHEK	skin
12	chr12:121363000-121364400	Enhancers	Esophagus	oesophagus
13	chr12:121363000-121364400	Enhancers	Placenta Amnion	Placenta Amnion
14	chr12:121363200-121364400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:121363200-121364400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:121363400-121363600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:121363400-121364400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:121363400-121364400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr12:121363400-121364400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr12:121363400-121364400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr12:121363400-121364400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:121363400-121364400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:121363400-121364400	Enhancers	HepG2	liver

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