Variant report

Variant	rs6490285
Chromosome Location	chr12:120547993-120547994
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120541333..120544024-chr12:120545087..120548824,4	K562	blood:
2	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
3	chr12:120530653..120533047-chr12:120546593..120548453,2	MCF-7	breast:
4	chr12:120539799..120542911-chr12:120545962..120548810,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135127	Chromatin interaction
ENSG00000111737	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2301883	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3759398	1.00[MEX][hapmap]
rs7135839	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7307130	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7312244	0.88[LWK][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes]
rs7316521	1.00[MEX][hapmap]
rs7954624	1.00[AFR][1000 genomes];1.00[AMR][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:120525800-120553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:120533800-120553000	Weak transcription	Fetal Kidney	kidney
4	chr12:120534400-120553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:120534600-120548200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:120539200-120552600	Weak transcription	Fetal Brain Male	brain
7	chr12:120539600-120551600	Weak transcription	Fetal Lung	lung
8	chr12:120539600-120552200	Strong transcription	Fetal Stomach	stomach
9	chr12:120540000-120553000	Weak transcription	HSMMtube	muscle
10	chr12:120541600-120548400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:120541600-120551000	Weak transcription	HSMM	muscle
12	chr12:120541800-120548800	Weak transcription	K562	blood
13	chr12:120541800-120552600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:120541800-120552800	Weak transcription	Brain Substantia Nigra	brain
15	chr12:120541800-120552800	Weak transcription	NH-A	brain
16	chr12:120542200-120553000	Weak transcription	Aorta	Aorta
17	chr12:120542400-120548200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:120542400-120552400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:120543000-120552800	Weak transcription	Osteobl	bone
20	chr12:120543200-120548200	Weak transcription	Small Intestine	intestine
21	chr12:120543400-120549000	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:120543400-120551600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:120543400-120552600	Weak transcription	Ovary	ovary
24	chr12:120543400-120553000	Weak transcription	Fetal Heart	heart
25	chr12:120543400-120553600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:120544000-120548400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:120544000-120548600	Weak transcription	HUVEC	blood vessel
28	chr12:120544000-120552800	Weak transcription	Colonic Mucosa	Colon
29	chr12:120544200-120552200	Weak transcription	Hela-S3	cervix
30	chr12:120544400-120548200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:120544400-120548200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:120544400-120548400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:120544400-120552800	Weak transcription	NHDF-Ad	bronchial
34	chr12:120544400-120553200	Strong transcription	Fetal Intestine Small	intestine
35	chr12:120544800-120548200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:120545400-120552800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:120545800-120549400	Enhancers	Left Ventricle	heart
38	chr12:120545800-120550000	Genic enhancers	Lung	lung
39	chr12:120546000-120548400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:120546000-120548400	Enhancers	Adipose Nuclei	Adipose
41	chr12:120546000-120550600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:120546200-120548000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:120546200-120548400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:120546200-120548600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:120546200-120550400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr12:120546400-120548200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr12:120546400-120548200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr12:120546400-120550400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr12:120546400-120552400	Weak transcription	HepG2	liver
50	chr12:120546400-120552800	Weak transcription	Placenta Amnion	Placenta Amnion

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