Variant report

Variant	rs12309301
Chromosome Location	chr12:104856807-104856808
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104849098..104852771-chr12:104856010..104858132,3	MCF-7	breast:
2	chr12:104850167..104852071-chr12:104856695..104858540,2	MCF-7	breast:
3	chr12:104852129..104854253-chr12:104856135..104858649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11112067	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112068	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320787	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12322339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1343928	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73382371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73382373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73382376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 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	chr12:104852800-104857400	Weak transcription	Psoas Muscle	Psoas
2	chr12:104853200-104868600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:104853400-104862200	Weak transcription	Gastric	stomach
4	chr12:104853400-104863000	Weak transcription	Pancreas	Pancrea
5	chr12:104853400-104863200	Weak transcription	Aorta	Aorta
6	chr12:104853600-104858200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:104853600-104858800	Weak transcription	Brain Angular Gyrus	brain
8	chr12:104853600-104867000	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:104853800-104870600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:104854000-104857600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:104854200-104862600	Weak transcription	Fetal Brain Female	brain
12	chr12:104854200-104867600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:104854800-104858800	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:104855000-104859200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:104855200-104857200	Weak transcription	Adipose Nuclei	Adipose
16	chr12:104855200-104859000	Weak transcription	Colonic Mucosa	Colon
17	chr12:104855200-104861200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:104855200-104861200	Enhancers	Fetal Thymus	thymus
19	chr12:104855200-104863800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:104855200-104868200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:104855200-104868600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:104855400-104857000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:104855400-104857200	Weak transcription	Fetal Brain Male	brain
24	chr12:104855400-104857200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:104855400-104857400	Weak transcription	Brain Anterior Caudate	brain
26	chr12:104855400-104857400	Weak transcription	Placenta	Placenta
27	chr12:104855400-104858800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:104855400-104859000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:104855400-104861400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:104855400-104862200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:104855400-104862800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:104855400-104863200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:104855400-104864800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:104855400-104866400	Weak transcription	Brain Germinal Matrix	brain
35	chr12:104855400-104874400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:104855400-104874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:104855600-104858200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:104855600-104860600	Weak transcription	HMEC	breast
39	chr12:104855600-104860800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:104856000-104857000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:104856000-104857800	Enhancers	HUVEC	blood vessel
42	chr12:104856000-104858000	Enhancers	Duodenum Mucosa	Duodenum
43	chr12:104856000-104858400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr12:104856000-104861600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:104856200-104857000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:104856200-104857400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:104856200-104857400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr12:104856200-104857600	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr12:104856200-104857600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:104856200-104857800	Flanking Active TSS	Primary T cells from cord blood	blood

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