Variant report

Variant	rs3884064
Chromosome Location	chr12:12526576-12526577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12519688..12522989-chr12:12524598..12527681,3	K562	blood:
2	chr12:12508497..12510863-chr12:12526548..12530591,3	MCF-7	breast:
3	chr12:12522631..12525556-chr12:12525783..12528472,2	MCF-7	breast:
4	chr12:12525607..12527513-chrX:39488072..39490988,2	MCF-7	breast:
5	chr12:12524724..12527440-chr12:12848940..12850671,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183150	Chromatin interaction
ENSG00000205791	Chromatin interaction
ENSG00000165714	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11829597	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2080519	1.00[CEU][hapmap]
rs2417181	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2417182	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2417183	0.82[EUR][1000 genomes]
rs2417184	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60914697	0.87[EUR][1000 genomes]
rs60951870	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61288717	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61923564	0.92[EUR][1000 genomes]
rs6488519	0.86[YRI][hapmap]
rs7136930	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7307285	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs73279335	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7979746	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1036040	chr12:12506839-12541869	Weak transcription Active TSS Enhancers Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases
4	nsv1037542	chr12:12506839-12542868	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1045637	chr12:12506839-12546747	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv1052243	chr12:12512726-12541869	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1051597	chr12:12513364-12541869	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv557584	chr12:12514203-12541869	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv818893	chr12:12515184-12541869	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1042425	chr12:12519319-12540455	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	nsv1050133	chr12:12519319-12541869	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1049869	chr12:12519319-12542868	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1047762	chr12:12520906-12541869	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12510800-12527400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:12510800-12528200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:12511400-12532600	Weak transcription	Fetal Lung	lung
4	chr12:12511400-12532800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:12511400-12535000	Weak transcription	Esophagus	oesophagus
6	chr12:12511400-12537800	Weak transcription	HSMMtube	muscle
7	chr12:12511400-12540600	Weak transcription	HSMM	muscle
8	chr12:12511600-12530200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:12511600-12532800	Weak transcription	Osteobl	bone
10	chr12:12511600-12540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:12511800-12526800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:12511800-12532600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:12512000-12532600	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:12512000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:12512200-12529800	Weak transcription	Fetal Kidney	kidney
17	chr12:12512200-12540400	Weak transcription	HMEC	breast
18	chr12:12512400-12540600	Weak transcription	Psoas Muscle	Psoas
19	chr12:12512800-12532600	Weak transcription	Hela-S3	cervix
20	chr12:12513000-12532600	Weak transcription	GM12878-XiMat	blood
21	chr12:12513200-12532400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:12516200-12537600	Weak transcription	Dnd41	blood
23	chr12:12516400-12529800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:12516400-12535200	Weak transcription	Lung	lung
25	chr12:12516400-12540000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:12518200-12531800	Weak transcription	Fetal Brain Female	brain
27	chr12:12519200-12529800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:12519200-12531400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr12:12519200-12532200	Weak transcription	Placenta	Placenta
30	chr12:12519200-12532600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
32	chr12:12519400-12532600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:12519400-12537400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:12519600-12540400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:12519800-12537600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:12520200-12529600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:12520200-12535000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:12520800-12532800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:12521000-12532600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:12521000-12532600	Weak transcription	Brain Anterior Caudate	brain
41	chr12:12521000-12532600	Weak transcription	Ovary	ovary
42	chr12:12521000-12538000	Weak transcription	Left Ventricle	heart
43	chr12:12521200-12529800	Weak transcription	Brain Angular Gyrus	brain
44	chr12:12521200-12532600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:12521800-12529400	Weak transcription	Brain Substantia Nigra	brain
46	chr12:12521800-12529800	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:12521800-12530200	Weak transcription	Thymus	Thymus
48	chr12:12521800-12531400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:12521800-12542800	Weak transcription	Adipose Nuclei	Adipose
50	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood

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