Variant report

Variant	rs297939
Chromosome Location	chr12:50319326-50319327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF3	chr12:50319175-50319472	GM12878	blood:	n/a	n/a
2	SUZ12	chr12:50319185-50319423	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:50319260-50319362	MCF-7	breast:	n/a	n/a
4	MYC	chr12:50319228-50319375	HUVEC	blood vessel:	n/a	n/a
5	MYC	chr12:50319265-50319354	MCF-7	breast:	n/a	n/a
6	MAX	chr12:50319291-50319364	NB4	blood:	n/a	n/a
7	CTCF	chr12:50319204-50319392	GM19239	blood:	n/a	n/a
8	TCF3	chr12:50319264-50319414	GM12878	blood:	n/a	n/a
9	CTCF	chr12:50319289-50319356	GM12892	blood:	n/a	n/a
10	MYC	chr12:50319253-50319411	MCF-7	breast:	n/a	n/a
11	BCL3	chr12:50319183-50319504	GM12878	blood:	n/a	n/a
12	BCL3	chr12:50319060-50319535	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:50319224-50319362	A549	lung:	n/a	n/a
14	MYC	chr12:50319303-50319390	GM12878	blood:	n/a	n/a
15	MYC	chr12:50319298-50319371	MCF-7	breast:	n/a	n/a
16	PBX3	chr12:50319140-50319475	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50305622..50307544-chr12:50317876..50320067,2	MCF-7	breast:
2	chr12:50314261..50315806-chr12:50318855..50321127,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2276187	0.83[ASN][1000 genomes]
rs2276188	0.85[ASN][1000 genomes]
rs420388	1.00[EUR][1000 genomes]
rs55984325	0.83[ASN][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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50313400-50320000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:50314800-50325000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:50315800-50319400	Enhancers	Adipose Nuclei	Adipose
4	chr12:50316000-50319400	Enhancers	Fetal Heart	heart
5	chr12:50316000-50319600	Enhancers	Fetal Muscle Leg	muscle
6	chr12:50316200-50321600	Weak transcription	Hela-S3	cervix
7	chr12:50316600-50333200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:50317800-50320000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:50318000-50319800	Enhancers	Spleen	Spleen
10	chr12:50318200-50319600	Weak transcription	Ovary	ovary
11	chr12:50318800-50326600	Weak transcription	Right Atrium	heart
12	chr12:50319200-50319400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:50319200-50319400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:50319200-50319400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr12:50319200-50319400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:50319200-50319400	ZNF genes & repeats	Fetal Brain Male	brain
17	chr12:50319200-50319400	Enhancers	Fetal Kidney	kidney
18	chr12:50319200-50319800	Enhancers	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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