Variant report

Variant	rs17860380
Chromosome Location	chr12:51721392-51721393
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51721324-51721877	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51475890..51478856-chr12:51719210..51722345,3	K562	blood:
2	chr12:51632967..51634708-chr12:51718961..51721755,2	K562	blood:
3	chr12:51712710..51714894-chr12:51720855..51723845,2	K562	blood:
4	chr12:51417902..51420501-chr12:51719275..51722211,2	K562	blood:
5	chr12:51710356..51713645-chr12:51720668..51723733,3	MCF-7	breast:
6	chr12:51663552..51665090-chr12:51718894..51721818,2	MCF-7	breast:
7	chr12:51720048..51722146-chr12:51747016..51749714,2	K562	blood:
8	chr12:51661800..51664432-chr12:51720431..51722225,2	K562	blood:
9	chr12:51712710..51716828-chr12:51719754..51724043,5	K562	blood:
10	chr12:51566806..51568529-chr12:51720798..51723312,2	K562	blood:

No data

Variant related genes	Relation type
BIN2	TF binding region
ENSG00000135457	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12578771	0.90[EUR][1000 genomes]
rs12580302	0.85[EUR][1000 genomes]
rs12581282	0.90[EUR][1000 genomes]
rs17860277	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17860287	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17860296	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17860302	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17860346	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860364	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860365	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860378	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860382	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17860387	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782470	0.83[EUR][1000 genomes]
rs3858637	0.81[EUR][1000 genomes]
rs4761870	0.81[EUR][1000 genomes]
rs55901988	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57484374	0.85[EUR][1000 genomes]
rs58213562	0.90[EUR][1000 genomes]
rs58673573	0.87[EUR][1000 genomes]
rs60641385	0.90[EUR][1000 genomes]
rs60797544	0.86[EUR][1000 genomes]
rs61172662	0.85[EUR][1000 genomes]
rs61380773	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61570206	0.90[EUR][1000 genomes]
rs61605107	0.87[EUR][1000 genomes]
rs7138394	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308177	0.82[EUR][1000 genomes]
rs7311196	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312857	0.87[EUR][1000 genomes]
rs7316221	0.82[EUR][1000 genomes]
rs7316301	0.87[EUR][1000 genomes]
rs7316604	0.82[EUR][1000 genomes]
rs74093810	0.82[EUR][1000 genomes]
rs74093814	0.82[EUR][1000 genomes]
rs74093823	0.85[EUR][1000 genomes]
rs74093827	0.85[EUR][1000 genomes]
rs74093853	0.94[EUR][1000 genomes]
rs7975715	0.82[EUR][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:63 , 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	chr12:51717600-51722600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:51717800-51722200	Weak transcription	Small Intestine	intestine
4	chr12:51718000-51722400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:51718000-51724400	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:51718000-51724400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:51718400-51722200	Enhancers	Primary T cells from cord blood	blood
8	chr12:51718400-51722400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:51718400-51722400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr12:51718400-51722600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr12:51718400-51723000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr12:51718400-51723200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:51718400-51723600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr12:51718400-51724400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:51718400-51724400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:51718400-51724400	Enhancers	Placenta	Placenta
17	chr12:51718400-51724400	Enhancers	Fetal Thymus	thymus
18	chr12:51718400-51727800	Weak transcription	Colonic Mucosa	Colon
19	chr12:51718600-51723000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr12:51719400-51723200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:51719600-51723200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr12:51719600-51723800	Enhancers	Dnd41	blood
23	chr12:51719800-51721400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:51719800-51724200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr12:51720000-51721400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:51720000-51721400	Enhancers	NHEK	skin
27	chr12:51720000-51722000	Enhancers	Liver	Liver
28	chr12:51720000-51722600	Enhancers	Brain Hippocampus Middle	brain
29	chr12:51720000-51723200	Enhancers	Thymus	Thymus
30	chr12:51720000-51723400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:51720200-51721400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:51720200-51721400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:51720200-51721400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr12:51720200-51721400	Enhancers	HMEC	breast
35	chr12:51720200-51721400	Flanking Active TSS	K562	blood
36	chr12:51720400-51721400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:51720400-51721400	Weak transcription	Spleen	Spleen
38	chr12:51720400-51721400	Flanking Active TSS	GM12878-XiMat	blood
39	chr12:51720600-51722000	Weak transcription	Right Atrium	heart
40	chr12:51720800-51728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:51720800-51735000	Weak transcription	Esophagus	oesophagus
42	chr12:51721000-51721400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr12:51721000-51722200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:51721000-51722400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr12:51721000-51723200	Weak transcription	Stomach Mucosa	stomach
46	chr12:51721000-51724200	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr12:51721000-51724400	Enhancers	Primary hematopoietic stem cells	blood
48	chr12:51721200-51721400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:51721200-51722200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr12:51721200-51722200	Weak transcription	Rectal Mucosa Donor 31	rectum

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