Variant report

Variant	rs17125635
Chromosome Location	chr12:51718789-51718790
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	POLR2A	chr12:51716760-51720317	K562	blood:	n/a	n/a
2	CEBPB	chr12:51718760-51719194	MCF-7	breast:	n/a	chr12:51718946-51718957
3	CEBPB	chr12:51718713-51719252	MCF-7	breast:	n/a	chr12:51718946-51718957

No.	Distal block	Cell Line	Cell type
1	chr12:51156096..51157796-chr12:51717451..51720427,2	MCF-7	breast:
2	chr12:51662477..51664063-chr12:51717292..51718857,2	MCF-7	breast:
3	chr12:51661913..51666807-chr12:51714627..51721165,8	MCF-7	breast:
4	chr12:51633168..51635077-chr12:51718759..51720463,2	MCF-7	breast:

Variant related genes	Relation type
BIN2	TF binding region
ENSG00000123268	Chromatin interaction
ENSG00000170545	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12298477	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12309916	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12317091	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12322804	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17860332	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17860384	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071453	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4026022	0.88[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7138439	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs72644880	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51711800-51721800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:51712800-51720200	Weak transcription	HMEC	breast
3	chr12:51713200-51720000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:51715000-51719000	Weak transcription	Stomach Mucosa	stomach
5	chr12:51715000-51720000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:51715000-51720000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:51715000-51720000	Weak transcription	Hela-S3	cervix
8	chr12:51715000-51720000	Weak transcription	HSMM	muscle
9	chr12:51715000-51720200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:51715000-51720200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:51715000-51720200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:51715200-51719800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:51715200-51720000	Weak transcription	HSMMtube	muscle
14	chr12:51715200-51720200	Weak transcription	NHDF-Ad	bronchial
15	chr12:51715200-51720400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:51715200-51720600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:51715600-51720200	Weak transcription	A549	lung
18	chr12:51715600-51720800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:51715800-51720200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:51715800-51720400	Weak transcription	Fetal Lung	lung
21	chr12:51715800-51720400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:51715800-51720600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:51716000-51720600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:51717600-51721000	Weak transcription	Brain Substantia Nigra	brain
25	chr12:51717600-51722600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:51717800-51719200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr12:51717800-51719800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:51717800-51720000	Weak transcription	Liver	Liver
29	chr12:51717800-51720000	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:51717800-51720000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:51717800-51720400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:51717800-51722200	Weak transcription	Small Intestine	intestine
33	chr12:51718000-51720200	Weak transcription	Right Atrium	heart
34	chr12:51718000-51720400	Enhancers	Spleen	Spleen
35	chr12:51718000-51722400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:51718000-51724400	Enhancers	Primary B cells from peripheral blood	blood
37	chr12:51718000-51724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:51718200-51719200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:51718200-51720000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:51718200-51720200	Enhancers	K562	blood
41	chr12:51718200-51720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:51718400-51719200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:51718400-51719400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:51718400-51719600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:51718400-51719800	Weak transcription	Adipose Nuclei	Adipose
46	chr12:51718400-51720200	Enhancers	Primary hematopoietic stem cells	blood
47	chr12:51718400-51720200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr12:51718400-51720400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:51718400-51720400	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:51718400-51720400	Enhancers	GM12878-XiMat	blood

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