Variant report

Variant	rs12304056
Chromosome Location	chr12:32361730-32361731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32359581..32362497-chr12:32406536..32409461,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12304066	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs161972	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16919377	1.00[AMR][1000 genomes]
rs2009380	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs55802552	1.00[AMR][1000 genomes]
rs57735320	1.00[AMR][1000 genomes]
rs58039881	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58186216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59313683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59549999	1.00[AMR][1000 genomes]
rs60994230	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294637	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs7295834	1.00[AMR][1000 genomes]
rs74072003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74072005	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74072006	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74074440	1.00[AMR][1000 genomes]
rs74074443	1.00[AMR][1000 genomes]
rs74074445	1.00[AMR][1000 genomes]
rs74074446	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7957620	1.00[AMR][1000 genomes]
rs7957784	1.00[AMR][1000 genomes]
rs7958620	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv983498	chr12:32153446-32388092	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS 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	10 gene(s)	inside rSNPs	diseases
5	nsv898969	chr12:32224948-32375677	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32293600-32369200	Weak transcription	Thymus	Thymus
2	chr12:32313400-32369400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:32323600-32373800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:32333400-32369200	Weak transcription	Left Ventricle	heart
5	chr12:32337000-32364800	Weak transcription	HSMM	muscle
6	chr12:32337000-32369000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:32337000-32369800	Weak transcription	Hela-S3	cervix
8	chr12:32348600-32375800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:32348800-32370400	Weak transcription	A549	lung
10	chr12:32350200-32364200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:32352000-32369000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:32352000-32369200	Weak transcription	Osteobl	bone
13	chr12:32352400-32363800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:32352400-32364000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:32352400-32364800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:32352400-32365000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:32352400-32369000	Weak transcription	Dnd41	blood
18	chr12:32352400-32369400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:32352400-32369400	Weak transcription	HMEC	breast
20	chr12:32353400-32369600	Weak transcription	NHDF-Ad	bronchial
21	chr12:32353600-32369400	Weak transcription	Primary B cells from cord blood	blood
22	chr12:32355400-32363800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:32355800-32363800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:32357600-32364000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:32357600-32370600	Weak transcription	Pancreas	Pancrea
26	chr12:32357800-32363800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:32357800-32363800	Weak transcription	Fetal Brain Female	brain
28	chr12:32357800-32365400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:32357800-32370600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:32358000-32369200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:32358800-32370600	Weak transcription	NHLF	lung
32	chr12:32359000-32363600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:32359000-32370200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:32359800-32361800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:32360000-32361800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr12:32360200-32362400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:32361200-32362600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:32361400-32363000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:32361400-32363000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:32361400-32363200	Enhancers	Ovary	ovary
41	chr12:32361600-32363400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr12:32361600-32369200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:32361600-32369200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:32361600-32371600	Weak transcription	Fetal Heart	heart

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