Variant report

Variant	rs12478924
Chromosome Location	chr2:38891387-38891388
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	CREB1	chr2:38891072-38891406	GM12878	blood:	n/a	n/a
2	NFIC	chr2:38890933-38891464	GM12878	blood:	n/a	n/a
3	FOS	chr2:38890999-38891405	MCF10A-Er-Src	breast:	n/a	chr2:38891021-38891030
4	FOXM1	chr2:38890889-38891475	GM12878	blood:	n/a	n/a
5	BATF	chr2:38890987-38891390	GM12878	blood:	n/a	n/a
6	STAT5A	chr2:38890967-38891395	GM12878	blood:	n/a	n/a
7	ATF2	chr2:38890859-38891427	GM12878	blood:	n/a	n/a
8	MEF2A	chr2:38890953-38891402	GM12878	blood:	n/a	chr2:38891021-38891029
9	RUNX3	chr2:38890901-38891428	GM12878	blood:	n/a	n/a
10	FOXM1	chr2:38890779-38891519	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:38890884-38891399	SK-N-MC	brain:	n/a	n/a
12	NFATC1	chr2:38890914-38891444	GM12878	blood:	n/a	n/a
13	EP300	chr2:38891048-38891392	GM12878	blood:	n/a	chr2:38891328-38891342
14	MTA3	chr2:38890861-38891441	GM12878	blood:	n/a	n/a
15	NFIC	chr2:38890805-38891536	GM12878	blood:	n/a	n/a
16	STAT3	chr2:38891011-38891510	MCF10A-Er-Src	breast:	n/a	n/a
17	MXI1	chr2:38890838-38891445	IMR90	lung:	n/a	n/a
18	BCLAF1	chr2:38890899-38891425	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38890666..38892556-chr2:38947054..38950004,2	K562	blood:
2	chr2:38881069..38883433-chr2:38890460..38892656,2	K562	blood:

Variant related genes	Relation type
GALM	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11688977	0.93[EUR][1000 genomes]
rs11689051	0.87[EUR][1000 genomes]
rs12712609	0.94[EUR][1000 genomes]
rs12712612	0.85[ASN][1000 genomes]
rs13011383	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13016907	0.83[ASN][1000 genomes]
rs13029674	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13032255	0.86[ASN][1000 genomes]
rs13383762	0.85[ASN][1000 genomes]
rs13387464	0.94[EUR][1000 genomes]
rs13425086	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17576472	0.85[ASN][1000 genomes]
rs17576507	0.83[ASN][1000 genomes]
rs2373424	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716236	0.87[ASN][1000 genomes]
rs34391548	0.85[ASN][1000 genomes]
rs34533539	0.88[EUR][1000 genomes]
rs34756536	0.83[ASN][1000 genomes]
rs34875979	0.81[ASN][1000 genomes]
rs3821023	0.94[EUR][1000 genomes]
rs4670262	0.94[ASN][1000 genomes]
rs4670263	0.94[EUR][1000 genomes]
rs4670882	0.92[EUR][1000 genomes]
rs4670883	0.92[EUR][1000 genomes]
rs4670885	0.83[ASN][1000 genomes]
rs58757994	0.83[ASN][1000 genomes]
rs6707543	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6732137	0.93[EUR][1000 genomes]
rs6736380	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6761563	0.94[EUR][1000 genomes]
rs7571326	0.93[EUR][1000 genomes]
rs7574493	0.92[EUR][1000 genomes]
rs7588762	0.92[EUR][1000 genomes]
rs7590750	0.94[EUR][1000 genomes]
rs7590835	0.94[EUR][1000 genomes]
rs7590926	0.94[EUR][1000 genomes]
rs7597535	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38882200-38892800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:38882800-38892800	Weak transcription	Thymus	Thymus
3	chr2:38886600-38892200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:38887600-38892600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:38888400-38892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:38888800-38892800	Weak transcription	HSMMtube	muscle
7	chr2:38889800-38891800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:38889800-38892800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:38889800-38892800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:38890200-38892200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:38890200-38892800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:38890200-38892800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:38890400-38892200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr2:38890400-38892400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:38890600-38891400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:38890600-38892600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:38890600-38892800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:38890800-38892600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:38890800-38892800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:38891000-38891800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:38891000-38891800	Enhancers	Osteobl	bone
22	chr2:38891000-38892000	Enhancers	HepG2	liver
23	chr2:38891000-38892400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:38891000-38892800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:38891200-38891400	Enhancers	GM12878-XiMat	blood
26	chr2:38891200-38891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:38891200-38891800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:38891200-38892200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:38891200-38892800	Enhancers	K562	blood

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