Variant report

Variant	rs12153966
Chromosome Location	chr6:13386748-13386749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13370709..13372780-chr6:13384931..13387341,2	K562	blood:
2	chr6:13383982..13388904-chr6:13485394..13488851,5	MCF-7	breast:
3	chr6:13371174..13372780-chr6:13384970..13387341,2	K562	blood:

Variant related genes	Relation type
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000187461	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10807431	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10807432	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10948650	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439536	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2496139	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2496160	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2496161	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2496162	0.96[CEU][hapmap]
rs2496173	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28813108	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711978	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs474159	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs476904	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs489396	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs491278	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492433	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501987	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs510932	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs516003	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs517803	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524118	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs531256	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs548119	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs552655	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs553671	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553948	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs560396	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs564174	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs570315	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs573109	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs575709	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs579028	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7760579	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7770078	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs821276	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs821277	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357708	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9367440	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS 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 miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:13376800-13395200	Weak transcription	NHEK	skin
4	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
5	chr6:13380200-13389400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:13381800-13395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
8	chr6:13383800-13395400	Weak transcription	Brain Anterior Caudate	brain
9	chr6:13384000-13386800	Weak transcription	Psoas Muscle	Psoas
10	chr6:13384000-13386800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:13384000-13387000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:13384000-13387000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:13384000-13395400	Weak transcription	Brain Substantia Nigra	brain
14	chr6:13384000-13395400	Weak transcription	NHLF	lung
15	chr6:13384200-13391000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:13384200-13395200	Weak transcription	Adipose Nuclei	Adipose
17	chr6:13384200-13395400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:13384200-13395400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:13384200-13395400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:13384600-13395400	Weak transcription	Primary B cells from cord blood	blood
21	chr6:13385000-13393200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:13385600-13390400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:13385600-13393000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:13385800-13390800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr6:13385800-13392200	Weak transcription	Right Ventricle	heart
26	chr6:13386400-13387000	Enhancers	Right Atrium	heart
27	chr6:13386600-13386800	Enhancers	Fetal Heart	heart
28	chr6:13386600-13386800	Enhancers	Lung	lung
29	chr6:13386600-13386800	Enhancers	Pancreas	Pancrea
30	chr6:13386600-13387000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:13386600-13387000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:13386600-13387000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:13386600-13387000	Enhancers	Left Ventricle	heart
34	chr6:13386600-13387200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:13386600-13387200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:13386600-13387200	Genic enhancers	Spleen	Spleen
37	chr6:13386600-13387200	ZNF genes & repeats	GM12878-XiMat	blood

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