Variant report

Variant	rs73307963
Chromosome Location	chr12:49682939-49682940
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:49682800-49682950	HMEC	breast:	n/a	n/a
2	CTCF	chr12:49682860-49683010	AG04450	lung:	n/a	n/a
3	SMC3	chr12:49681775-49683027	SK-N-SH	brain:	n/a	chr12:49682882-49682890 chr12:49682287-49682301
4	ZNF263	chr12:49681852-49683145	HEK293-T-REx	kidney:	n/a	n/a
5	CTCF	chr12:49682840-49682990	GM12867	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49681725..49683047-chr12:49690017..49691263,7	K562	blood:
2	chr12:49674974..49678602-chr12:49682204..49684622,3	MCF-7	breast:
3	chr12:49681842..49683325-chr12:49740711..49741813,10	K562	blood:
4	chr12:49674656..49677388-chr12:49681241..49683027,2	K562	blood:
5	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
6	chr12:49680157..49683584-chr12:49686626..49689914,4	K562	blood:
7	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
8	chr12:49681953..49682967-chr12:49730581..49731487,4	K562	blood:
9	chr12:49681895..49684314-chr12:49959799..49961402,2	MCF-7	breast:
10	chr12:49670426..49673698-chr12:49680662..49684493,5	K562	blood:
11	chr12:49682752..49684586-chr12:49760738..49763560,2	K562	blood:
12	chr12:49657412..49661097-chr12:49680173..49683104,4	MCF-7	breast:
13	chr12:49681373..49684532-chr12:49689640..49692033,4	MCF-7	breast:
14	chr12:49677107..49685653-chr12:49686694..49692276,10	MCF-7	breast:
15	chr12:49681072..49683982-chr12:49740042..49742120,4	MCF-7	breast:
16	chr12:49681784..49683022-chr12:49735866..49736958,14	K562	blood:
17	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
18	chr12:49665631..49676200-chr12:49678297..49684493,17	K562	blood:
19	chr12:49682080..49684336-chr12:49718249..49720945,2	MCF-7	breast:
20	chr12:49668368..49669871-chr12:49682424..49685316,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1QL4-2	chr12:49682852-49683068	XLOC_010069

No data

Variant related genes	Relation type
PRPH	TF binding region
ENSG00000123352	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000178401	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12299403	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12299406	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73307948	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73309973	0.82[AMR][1000 genomes]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	esv19135	chr12:49676002-49690399	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv558834	chr12:49676010-49691567	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73307963	C1QL4	cis	Thyroid	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49678200-49686800	Weak transcription	HSMM	muscle
2	chr12:49682000-49683200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:49682200-49686800	Weak transcription	HSMMtube	muscle
4	chr12:49682400-49683200	Enhancers	NHEK	skin
5	chr12:49682400-49683400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:49682400-49683400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:49682400-49683400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:49682400-49683400	Enhancers	HMEC	breast
9	chr12:49682600-49683000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:49682800-49683000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:49682800-49683000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:49682800-49683000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:49682800-49686800	Weak transcription	Hela-S3	cervix
14	chr12:49682800-49687000	Weak transcription	Right Atrium	heart

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