Variant report

Variant	rs776340
Chromosome Location	chr12:57875468-57875469
allele	C/G
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	chr12:57875437-57875549	K562	blood:	n/a	chr12:57875476-57875487
2	MAX	chr12:57875443-57875487	NB4	blood:	n/a	n/a
3	CEBPB	chr12:57875360-57875631	HepG2	liver:	n/a	chr12:57875476-57875487
4	MYC	chr12:57875406-57875552	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57872773..57878513-chr12:57879040..57886839,8	K562	blood:
2	chr12:57852970..57855584-chr12:57874949..57877161,2	K562	blood:
3	chr12:57870455..57873151-chr12:57875417..57876991,2	K562	blood:
4	chr12:57874621..57876304-chr12:57881032..57883463,2	MCF-7	breast:

Variant related genes	Relation type
ARHGAP9	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000111087	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1148550	1.00[EUR][1000 genomes]
rs1284467	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1679366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2620680	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs537161	1.00[EUR][1000 genomes]
rs59235552	1.00[EUR][1000 genomes]
rs60374392	1.00[EUR][1000 genomes]
rs703833	1.00[EUR][1000 genomes]
rs703840	1.00[EUR][1000 genomes]
rs775325	1.00[EUR][1000 genomes]
rs7973639	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak 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	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv819781	chr12:57873564-57882217	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57871600-57881200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:57871600-57881200	Weak transcription	Right Atrium	heart
3	chr12:57872000-57877000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:57872400-57875800	Enhancers	Fetal Thymus	thymus
5	chr12:57873200-57881200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:57873400-57877400	Weak transcription	Placenta	Placenta
7	chr12:57873600-57875800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:57873600-57881000	Weak transcription	Dnd41	blood
9	chr12:57874000-57875800	Enhancers	Primary T cells from cord blood	blood
10	chr12:57874000-57875800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr12:57874000-57875800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:57874000-57875800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:57874000-57875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:57874000-57875800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:57874000-57876000	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:57874000-57876000	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:57874000-57876000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:57874000-57876000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:57874000-57876200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:57874000-57881200	Weak transcription	Thymus	Thymus
21	chr12:57874200-57876000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr12:57874200-57876200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr12:57874400-57876000	Enhancers	Primary B cells from cord blood	blood
24	chr12:57874600-57881000	Weak transcription	Spleen	Spleen
25	chr12:57874800-57875800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:57874800-57876000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:57874800-57876000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:57875000-57875600	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:57875000-57877200	Weak transcription	GM12878-XiMat	blood
30	chr12:57875000-57881200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:57875400-57875600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:57875400-57875600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr12:57875400-57875600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr12:57875400-57875600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr12:57875400-57875600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr12:57875400-57875800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr12:57875400-57875800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:57875400-57875800	Enhancers	K562	blood
39	chr12:57875400-57876000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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