Variant report

Variant	rs560396
Chromosome Location	chr6:13384183-13384184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13384119..13385773-chr6:13487475..13489229,2	MCF-7	breast:
2	chr6:13383672..13384260-chr6:13527976..13528686,2	MCF-7	breast:
3	chr6:13383982..13388904-chr6:13485394..13488851,5	MCF-7	breast:
4	chr6:13383495..13385578-chr6:13393149..13396280,3	K562	blood:
5	chr6:13379696..13382625-chr6:13383447..13385433,2	MCF-7	breast:

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	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10807432	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10948650	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12153966	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439536	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496139	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2496160	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2496161	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2496162	0.86[EUR][1000 genomes]
rs2496173	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28813108	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711978	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs474159	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs476904	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489396	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs492433	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501987	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs510932	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs516003	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs517803	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524118	0.96[EUR][1000 genomes]
rs531256	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs548119	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552655	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs553671	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs553948	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs564174	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs570315	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs573109	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs575709	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs579028	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7760579	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770078	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821276	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs821277	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357708	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367440	0.87[EUR][1000 genomes];0.87[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:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13365800-13385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:13368400-13386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:13376800-13386600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:13376800-13395200	Weak transcription	NHEK	skin
7	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
8	chr6:13379200-13386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:13380200-13389400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:13381000-13385800	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:13381800-13384600	Enhancers	Primary B cells from cord blood	blood
12	chr6:13381800-13395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:13382000-13385200	Weak transcription	K562	blood
14	chr6:13382000-13386600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:13382200-13384200	Weak transcription	Left Ventricle	heart
16	chr6:13382200-13384800	Weak transcription	Right Atrium	heart
17	chr6:13382400-13386600	Weak transcription	Lung	lung
18	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
19	chr6:13382800-13384600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr6:13382800-13385600	Enhancers	Liver	Liver
21	chr6:13383200-13384200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:13383200-13384200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr6:13383200-13384600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:13383400-13384200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:13383400-13384200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:13383400-13384200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:13383400-13384200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:13383400-13384200	Enhancers	Adipose Nuclei	Adipose
29	chr6:13383400-13384200	Enhancers	A549	lung
30	chr6:13383400-13384400	Enhancers	Stomach Smooth Muscle	stomach
31	chr6:13383400-13384800	Enhancers	Colon Smooth Muscle	Colon
32	chr6:13383400-13385000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr6:13383400-13385600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:13383400-13385800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:13383400-13385800	Enhancers	Fetal Heart	heart
36	chr6:13383400-13386000	Enhancers	Stomach Mucosa	stomach
37	chr6:13383600-13384200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:13383600-13384200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:13383600-13384200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:13383600-13384200	Enhancers	Fetal Stomach	stomach
41	chr6:13383600-13384200	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr6:13383600-13384200	Enhancers	HepG2	liver
43	chr6:13383600-13384400	Enhancers	Spleen	Spleen
44	chr6:13383600-13385000	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr6:13383800-13384200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr6:13383800-13384200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:13383800-13384400	Enhancers	Colonic Mucosa	Colon
48	chr6:13383800-13384400	Enhancers	GM12878-XiMat	blood
49	chr6:13383800-13384800	Weak transcription	Fetal Kidney	kidney
50	chr6:13383800-13384800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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