Variant report

Variant	rs3858534
Chromosome Location	chr12:75947084-75947085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75946731..75948885-chr12:75954512..75956708,2	MCF-7	breast:
2	chr12:75936274..75938020-chr12:75944642..75947136,2	MCF-7	breast:
3	chr12:75942170..75945016-chr12:75945671..75947951,2	MCF-7	breast:
4	chr12:75904950..75907035-chr12:75944732..75947463,2	K562	blood:

Variant related genes	Relation type
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10879928	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1148003	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148004	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148005	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148006	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1275474	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1679381	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795379	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1824980	0.87[ASN][1000 genomes]
rs1824982	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2366987	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3847669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75938600-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:75942800-75947400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:75942800-75947400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:75943000-75947200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:75943000-75947200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:75944400-75947400	Weak transcription	A549	lung
7	chr12:75944400-75947600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:75944600-75947200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:75944600-75947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:75944600-75947200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:75944600-75947200	Weak transcription	NH-A	brain
12	chr12:75944800-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:75944800-75947400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:75944800-75948200	Weak transcription	Lung	lung
15	chr12:75944800-75948200	Weak transcription	Right Atrium	heart
16	chr12:75944800-75954000	Weak transcription	Pancreas	Pancrea
17	chr12:75945000-75947200	Weak transcription	NHDF-Ad	bronchial
18	chr12:75945000-75947400	Weak transcription	Adipose Nuclei	Adipose
19	chr12:75945000-75947400	Weak transcription	NHLF	lung
20	chr12:75945200-75947200	Weak transcription	Fetal Lung	lung
21	chr12:75945200-75947200	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:75945200-75947400	Weak transcription	Fetal Kidney	kidney
23	chr12:75945400-75947200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:75945400-75947400	Weak transcription	HSMM	muscle
25	chr12:75945400-75948800	Enhancers	Fetal Heart	heart
26	chr12:75945800-75947200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:75945800-75947600	Weak transcription	Fetal Stomach	stomach
28	chr12:75946200-75947200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:75946200-75947400	Enhancers	HSMMtube	muscle
30	chr12:75946200-75947600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr12:75946400-75947400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:75946400-75947400	Enhancers	Fetal Brain Female	brain
33	chr12:75946600-75957600	Weak transcription	Fetal Brain Male	brain
34	chr12:75946800-75947800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:75946800-75948200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr12:75947000-75947200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:75947000-75948000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:75947000-75948600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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