Variant report

Variant	rs59021370
Chromosome Location	chr2:98307712-98307713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:98307608-98307944	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr2:98307643-98307990	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA3	chr2:98307590-98308935	MCF-7	breast:	n/a	n/a
4	ZNF143	chr2:98307652-98308049	H1-hESC	embryonic stem cell:	n/a	n/a
5	GATA3	chr2:98307709-98308215	MCF-7	breast:	n/a	n/a
6	SIN3A	chr2:98307643-98307953	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr2:98307563-98308045	H1-hESC	embryonic stem cell:	n/a	chr2:98307819-98307830
8	GTF2F1	chr2:98307688-98307888	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr2:98307610-98308062	H1-hESC	embryonic stem cell:	n/a	chr2:98307839-98307848
10	TBP	chr2:98307689-98307943	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD2	chr2:98307618-98307960	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr2:98307565-98308110	ECC-1	luminal epithelium:	n/a	chr2:98307839-98307848
13	GATA3	chr2:98307510-98308194	MCF-7	breast:	n/a	n/a
14	CTBP2	chr2:98307565-98308295	H1-hESC	embryonic stem cell:	n/a	n/a
15	TCF12	chr2:98307575-98308007	H1-hESC	embryonic stem cell:	n/a	n/a
16	TCF12	chr2:98307479-98308133	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr2:98307573-98307868	ECC-1	luminal epithelium:	n/a	n/a
18	TEAD4	chr2:98307607-98308119	ECC-1	luminal epithelium:	n/a	chr2:98307839-98307848
19	TEAD4	chr2:98307618-98308005	H1-hESC	embryonic stem cell:	n/a	chr2:98307839-98307848

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98262433..98263983-chr2:98307567..98310262,2	MCF-7	breast:
2	chr2:98279098..98281561-chr2:98304916..98307735,3	MCF-7	breast:
3	chr2:98278665..98281371-chr2:98305087..98308005,4	MCF-7	breast:
4	chr2:98307215..98309904-chr2:98310640..98314213,3	K562	blood:

No data

No data

No data

Variant related genes	Relation type
LINC01125	TF binding region
ENSG00000228486	Chromatin interaction
ENSG00000201806	Chromatin interaction
ENSG00000115073	Chromatin interaction
ENSG00000135940	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17028771	0.94[ASN][1000 genomes]
rs17695937	0.89[ASN][1000 genomes]
rs2071038	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290123	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290126	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290127	0.94[ASN][1000 genomes]
rs34459720	0.94[ASN][1000 genomes]
rs35321033	0.94[ASN][1000 genomes]
rs35530168	0.94[ASN][1000 genomes]
rs55757705	0.94[ASN][1000 genomes]
rs55766309	0.94[ASN][1000 genomes]
rs55933640	0.94[ASN][1000 genomes]
rs56035334	0.94[ASN][1000 genomes]
rs56233535	0.94[ASN][1000 genomes]
rs56717024	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58321192	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58383658	0.91[ASN][1000 genomes]
rs59060391	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59168350	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60226695	1.00[EUR][1000 genomes]
rs62157581	0.94[ASN][1000 genomes]
rs6542982	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6753752	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72951131	1.00[ASN][1000 genomes]
rs7425883	0.94[ASN][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	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
2	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
3	esv1829350	chr2:98170405-98315611	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98281000-98323800	Weak transcription	Gastric	stomach
2	chr2:98292200-98317800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98305600-98313600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:98306000-98322400	Weak transcription	Fetal Stomach	stomach
5	chr2:98306200-98307800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:98307000-98313400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:98307400-98308400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:98307600-98307800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:98307600-98308200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr2:98307600-98308200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr2:98307600-98308200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:98307600-98308200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:98307600-98308200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:98307600-98308200	Enhancers	HMEC	breast
15	chr2:98307600-98308400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr2:98307600-98308600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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