Variant report

Variant	rs58870360
Chromosome Location	chr3:118864723-118864724
allele	C/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	CTCF	chr3:118864662-118864747	GM12892	blood:	n/a	n/a
2	RAD21	chr3:118863976-118864821	SK-N-SH	brain:	n/a	chr3:118864399-118864418 chr3:118864401-118864408
3	MAX	chr3:118864277-118864875	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr3:118864110-118864763	A549	lung:	n/a	chr3:118864624-118864631
5	CTCF	chr3:118864640-118864790	BJ	skin:	n/a	n/a
6	MYC	chr3:118864686-118864902	MCF-7	breast:	n/a	n/a
7	ZNF143	chr3:118864245-118864762	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:118864580-118864730	SK-N-SH_RA	brain:	n/a	n/a
9	E2F6	chr3:118864121-118864871	A549	lung:	n/a	chr3:118864459-118864471
10	CTCF	chr3:118864080-118864785	SK-N-SH	brain:	n/a	chr3:118864400-118864421 chr3:118864398-118864416 chr3:118864401-118864414 chr3:118864403-118864411 chr3:118864399-118864415
11	CTCF	chr3:118864680-118864830	HMEC	breast:	n/a	n/a
12	MAX	chr3:118864122-118864930	A549	lung:	n/a	n/a
13	USF2	chr3:118864298-118864939	H1-hESC	embryonic stem cell:	n/a	chr3:118864471-118864482
14	CTCF	chr3:118864660-118864810	HVMF	connective:	n/a	n/a
15	E2F6	chr3:118864168-118864882	H1-hESC	embryonic stem cell:	n/a	chr3:118864459-118864471
16	CTCF	chr3:118863990-118864849	A549	lung:	n/a	chr3:118864400-118864421 chr3:118864398-118864416 chr3:118864401-118864414 chr3:118864403-118864411 chr3:118864399-118864415
17	RAD21	chr3:118864078-118864796	A549	lung:	n/a	chr3:118864399-118864418 chr3:118864401-118864408
18	RAD21	chr3:118864117-118864814	H1-hESC	embryonic stem cell:	n/a	chr3:118864399-118864418 chr3:118864401-118864408
19	RAD21	chr3:118864179-118864732	MCF-7	breast:	n/a	chr3:118864399-118864418 chr3:118864401-118864408
20	POLR2A	chr3:118864677-118865020	MCF-7	breast:	n/a	n/a
21	CTCF	chr3:118864600-118864750	HMF	breast:	n/a	n/a
22	SMC3	chr3:118864009-118864789	SK-N-SH	brain:	n/a	chr3:118864400-118864414
23	CTCF	chr3:118864700-118864850	GM12864	blood:	n/a	n/a
24	E2F6	chr3:118864324-118864884	H1-hESC	embryonic stem cell:	n/a	chr3:118864459-118864471
25	CTCF	chr3:118864640-118864790	GM12868	blood:	n/a	n/a
26	CTCF	chr3:118864698-118864735	GM12891	blood:	n/a	n/a
27	MAX	chr3:118864177-118864783	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:118863219..118864917-chr3:118959824..118960983,11	MCF-7	breast:
2	chr3:118864109..118864821-chr3:118925347..118925976,3	MCF-7	breast:
3	chr3:118863527..118866220-chr3:118958408..118962544,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B4GALT4-2	chr3:118864660-118864840	NONHSAT091373

Variant related genes	Relation type
C3orf30	TF binding region
ENSG00000251012	TF binding region
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10934484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347449	0.95[ASN][1000 genomes]
rs251450	0.80[ASN][1000 genomes]
rs251451	0.80[ASN][1000 genomes]
rs2573193	0.95[ASN][1000 genomes]
rs4133080	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55906068	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56130435	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56314227	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56317615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60930913	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73185873	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs73185893	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73185896	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73185901	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829692	chr3:118727772-118901711	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118863800-118865200	Enhancers	A549	lung
2	chr3:118864000-118864800	Enhancers	Stomach Mucosa	stomach
3	chr3:118864200-118864800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:118864400-118864800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:118864400-118864800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:118864400-118864800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:118864400-118864800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:118864400-118864800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:118864400-118864800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:118864400-118864800	Enhancers	Fetal Intestine Small	intestine
11	chr3:118864400-118864800	Enhancers	Gastric	stomach
12	chr3:118864400-118864800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr3:118864400-118864800	Enhancers	Right Ventricle	heart
14	chr3:118864400-118864800	Enhancers	HMEC	breast
15	chr3:118864400-118865000	Enhancers	Placenta	Placenta
16	chr3:118864400-118865000	Enhancers	K562	blood
17	chr3:118864600-118864800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:118864600-118865200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:118864600-118865200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:118864600-118865600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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