Variant report

Variant	rs56007954
Chromosome Location	chr12:32410882-32410883
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	chr12:32111261..32114014-chr12:32410835..32414194,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174718	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11051866	1.00[ASN][1000 genomes]
rs12296246	0.91[EUR][1000 genomes]
rs12297959	0.91[EUR][1000 genomes]
rs12298558	0.91[EUR][1000 genomes]
rs12307792	0.91[EUR][1000 genomes]
rs12308522	0.86[EUR][1000 genomes]
rs12310014	0.86[EUR][1000 genomes]
rs12310030	0.86[EUR][1000 genomes]
rs12312114	0.91[EUR][1000 genomes]
rs12317202	0.86[EUR][1000 genomes]
rs16916339	0.91[EUR][1000 genomes]
rs16919525	0.86[EUR][1000 genomes]
rs16919527	0.86[EUR][1000 genomes]
rs28427470	0.91[EUR][1000 genomes]
rs55766406	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075891	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56235810	1.00[ASN][1000 genomes]
rs56254678	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58801621	0.91[EUR][1000 genomes]
rs59032949	0.86[EUR][1000 genomes]
rs6488039	0.91[EUR][1000 genomes]
rs7134330	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136736	0.91[EUR][1000 genomes]
rs7136837	0.91[EUR][1000 genomes]
rs7136969	0.91[EUR][1000 genomes]
rs7137031	0.91[EUR][1000 genomes]
rs7137148	0.89[EUR][1000 genomes]
rs73310707	0.86[EUR][1000 genomes]
rs73310709	0.86[EUR][1000 genomes]
rs73310720	0.86[EUR][1000 genomes]
rs73310737	0.91[EUR][1000 genomes]
rs7956048	0.91[EUR][1000 genomes]
rs7957547	0.86[EUR][1000 genomes]
rs7959439	0.86[EUR][1000 genomes]
rs7962134	0.91[EUR][1000 genomes]
rs7970958	0.86[EUR][1000 genomes]
rs7971625	0.86[EUR][1000 genomes]
rs7974961	0.91[EUR][1000 genomes]
rs7977350	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32393600-32423800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:32394000-32424200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:32394400-32423800	Weak transcription	NH-A	brain
4	chr12:32394600-32414400	Weak transcription	HUVEC	blood vessel
5	chr12:32402000-32417800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:32402000-32424000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:32402400-32423600	Weak transcription	Osteobl	bone
8	chr12:32403000-32417800	Weak transcription	Brain Angular Gyrus	brain
9	chr12:32403000-32417800	Weak transcription	Fetal Stomach	stomach
10	chr12:32403000-32424400	Weak transcription	HSMMtube	muscle
11	chr12:32403200-32411800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:32403200-32413400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:32403200-32417600	Weak transcription	NHDF-Ad	bronchial
14	chr12:32403200-32424000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:32403200-32424400	Weak transcription	HSMM	muscle
16	chr12:32403400-32411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:32403400-32413800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:32403400-32423600	Weak transcription	Brain Germinal Matrix	brain
19	chr12:32403800-32414400	Weak transcription	HMEC	breast
20	chr12:32404600-32411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:32405000-32423800	Weak transcription	Left Ventricle	heart
22	chr12:32405400-32414200	Weak transcription	Spleen	Spleen
23	chr12:32405400-32417800	Weak transcription	Thymus	Thymus
24	chr12:32405600-32423200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:32405600-32423800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:32405800-32413200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:32406000-32418000	Weak transcription	Ovary	ovary
28	chr12:32406200-32417800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:32406600-32417800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:32407000-32423600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:32407400-32417800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:32407800-32423400	Weak transcription	Brain Anterior Caudate	brain
33	chr12:32408200-32424000	Weak transcription	Hela-S3	cervix
34	chr12:32408200-32425600	Weak transcription	Primary T cells from cord blood	blood
35	chr12:32408400-32413800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:32409400-32423600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:32409400-32423800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:32409600-32414600	Weak transcription	Fetal Thymus	thymus
39	chr12:32410000-32411000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:32410400-32411200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:32410400-32411200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
42	chr12:32410400-32411200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:32410400-32411200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:32410400-32411600	ZNF genes & repeats	GM12878-XiMat	blood
45	chr12:32410600-32411200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:32410600-32411200	ZNF genes & repeats	Primary B cells from cord blood	blood
47	chr12:32410600-32411600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr12:32410800-32411000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
49	chr12:32410800-32411000	Strong transcription	Dnd41	blood
50	chr12:32410800-32411000	Active TSS	K562	blood

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