Variant report

Variant	rs2449476
Chromosome Location	chr12:56146015-56146016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56134722..56138691-chr12:56142013..56149652,14	MCF-7	breast:
2	chr12:56132326..56134281-chr12:56145897..56148451,2	K562	blood:
3	chr12:56143361..56145191-chr12:56145482..56147096,2	K562	blood:
4	chr12:56145012..56148000-chr12:56170304..56172255,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135414	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1466512	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs1681085	1.00[AMR][1000 genomes]
rs1725358	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1871999	1.00[AMR][1000 genomes]
rs2462938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2694008	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2694015	1.00[AMR][1000 genomes]
rs2887997	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4759012	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4759202	1.00[AMR][1000 genomes]
rs55884432	1.00[AMR][1000 genomes]
rs6581083	1.00[AMR][1000 genomes]
rs7294345	1.00[AMR][1000 genomes]
rs7305623	1.00[MEX][hapmap]
rs7310325	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772250	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772251	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs772252	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772256	1.00[AMR][1000 genomes]
rs772257	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772259	1.00[AMR][1000 genomes]
rs772260	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs772261	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7956337	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7963379	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs812230	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak 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 target site	78 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	chr12:56138200-56150800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:56138800-56146200	Weak transcription	Small Intestine	intestine
3	chr12:56139200-56149000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:56139400-56150000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:56139400-56174600	Weak transcription	Stomach Mucosa	stomach
6	chr12:56140400-56151200	Weak transcription	Psoas Muscle	Psoas
7	chr12:56141000-56148800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:56141400-56151400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:56141400-56151400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:56141400-56152400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56141600-56152400	Strong transcription	Fetal Stomach	stomach
12	chr12:56141600-56161400	Strong transcription	Primary T cells from cord blood	blood
13	chr12:56141800-56148400	Strong transcription	Fetal Intestine Small	intestine
14	chr12:56141800-56151600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:56141800-56152400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:56141800-56153600	Strong transcription	Fetal Brain Female	brain
17	chr12:56141800-56157600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:56141800-56158000	Strong transcription	Fetal Intestine Large	intestine
19	chr12:56142000-56148000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:56142000-56148000	Strong transcription	Brain Germinal Matrix	brain
21	chr12:56142000-56154200	Strong transcription	Primary B cells from cord blood	blood
22	chr12:56142000-56191800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:56142200-56148400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:56142200-56148400	Strong transcription	Spleen	Spleen
25	chr12:56142200-56161000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr12:56142200-56162000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:56142400-56146600	Strong transcription	Aorta	Aorta
28	chr12:56142400-56147000	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr12:56142400-56147200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:56142400-56148400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:56142400-56148400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:56142400-56154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:56142400-56155400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr12:56142400-56155800	Strong transcription	NHLF	lung
35	chr12:56142400-56157400	Strong transcription	Thymus	Thymus
36	chr12:56142400-56161400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:56142600-56147400	Strong transcription	Brain Anterior Caudate	brain
38	chr12:56142600-56149400	Strong transcription	Brain Cingulate Gyrus	brain
39	chr12:56142600-56157600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:56142600-56157600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:56142600-56158000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:56142600-56161000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:56142600-56161200	Strong transcription	Dnd41	blood
44	chr12:56142600-56162000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:56142800-56146600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr12:56142800-56147200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:56142800-56148600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr12:56142800-56154600	Strong transcription	Placenta	Placenta
49	chr12:56142800-56154600	Strong transcription	Osteobl	bone
50	chr12:56142800-56158200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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