Variant report

Variant	rs7325969
Chromosome Location	chr13:76119506-76119507
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr13:76119008-76119530	Hela-S3	cervix:	n/a	chr13:76119247-76119258 chr13:76119186-76119203
2	MYC	chr13:76119056-76119511	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76118168..76119687-chr13:76122527..76125250,2	MCF-7	breast:
2	chr13:76109687..76114004-chr13:76118514..76122227,3	K562	blood:

Variant related genes	Relation type
ENSG00000261553	TF binding region
UCHL3	TF binding region
ENSG00000188243	Chromatin interaction
ENSG00000118939	Chromatin interaction
ENSG00000261553	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1050235	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs12859594	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12859711	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12861744	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12861774	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12865529	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs12866747	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12869081	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs12870619	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12871445	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17064647	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2031234	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34072684	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34241221	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34407556	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34572351	0.85[EUR][1000 genomes]
rs34949196	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35132045	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35132275	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35352582	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35556048	0.94[EUR][1000 genomes]
rs35596538	0.94[EUR][1000 genomes]
rs35631959	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35680815	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35797826	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35853105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35901810	0.96[EUR][1000 genomes]
rs36043532	0.85[EUR][1000 genomes]
rs4885299	0.87[GIH][hapmap]
rs4885302	0.85[EUR][1000 genomes]
rs4885303	0.85[EUR][1000 genomes]
rs4885304	0.85[EUR][1000 genomes]
rs4885310	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885311	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4885315	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4885327	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6562904	0.85[EUR][1000 genomes]
rs6562910	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6562911	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66528354	0.84[EUR][1000 genomes]
rs66635712	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66808557	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67051742	0.94[EUR][1000 genomes]
rs67211435	0.85[EUR][1000 genomes]
rs67270540	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67532736	0.85[EUR][1000 genomes]
rs67656352	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68017902	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68044755	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68052366	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71215998	0.85[EUR][1000 genomes]
rs7321611	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7324560	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7337186	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7986201	0.92[EUR][1000 genomes]
rs9530443	0.85[EUR][1000 genomes]
rs9530444	0.85[EUR][1000 genomes]
rs9543950	0.85[EUR][1000 genomes]
rs9543952	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs9543953	0.83[EUR][1000 genomes]
rs9543961	0.85[EUR][1000 genomes]
rs9543962	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv900564	chr13:76100090-76156136	Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	esv3326553	chr13:76106251-76120849	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv14404	chr13:76107773-76119573	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2421984	chr13:76111280-76119506	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv525594	chr13:76111280-76119506	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv818980	chr13:76111280-76119506	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv900565	chr13:76111280-76169347	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv3350275	chr13:76113551-76120649	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
12	esv3428782	chr13:76113751-76120749	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7325969	LMO7	cis	parietal	SCAN
rs7325969	UCHL3	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76112200-76123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:76112600-76122800	Weak transcription	Fetal Brain Male	brain
3	chr13:76112600-76123000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:76112600-76123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:76112600-76123600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:76112800-76122800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:76112800-76122800	Weak transcription	Brain Anterior Caudate	brain
8	chr13:76112800-76123000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:76112800-76123000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:76112800-76123000	Weak transcription	Adipose Nuclei	Adipose
11	chr13:76115600-76120200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr13:76115800-76120400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:76116000-76123000	Weak transcription	GM12878-XiMat	blood
14	chr13:76116400-76123200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr13:76116600-76119600	Enhancers	HepG2	liver
16	chr13:76117800-76119600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:76118600-76119600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr13:76118600-76119600	Enhancers	NHDF-Ad	bronchial
19	chr13:76118600-76119600	Enhancers	Osteobl	bone
20	chr13:76118600-76120000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr13:76118800-76120000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:76119000-76119600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:76119000-76119600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:76119000-76119600	Enhancers	Hela-S3	cervix
25	chr13:76119000-76119600	Enhancers	HMEC	breast
26	chr13:76119000-76119600	Enhancers	NHEK	skin
27	chr13:76119000-76120000	Enhancers	Placenta	Placenta
28	chr13:76119000-76121000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr13:76119200-76119600	Enhancers	NHLF	lung
30	chr13:76119200-76119800	Enhancers	K562	blood
31	chr13:76119200-76120000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr13:76119200-76120000	Enhancers	Psoas Muscle	Psoas
33	chr13:76119400-76119600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr13:76119400-76123000	Weak transcription	Fetal Kidney	kidney
35	chr13:76119400-76123000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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