Variant report

Variant	rs488885
Chromosome Location	chr6:13391887-13391888
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	chr6:13379945..13382317-chr6:13389702..13392053,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11753720	0.80[ASN][1000 genomes]
rs1345031	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1345032	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1837701	0.80[ASN][1000 genomes]
rs2119483	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2119484	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4454121	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4715251	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4715261	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs476138	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs478630	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs478804	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs480648	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs485804	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs490443	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs500197	0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs500293	0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs503117	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs508153	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs513613	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs519657	0.93[EUR][1000 genomes]
rs519890	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs520828	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs523221	0.80[ASN][1000 genomes]
rs536916	0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs536998	0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs544639	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs546507	0.85[ASN][1000 genomes]
rs550403	0.85[EUR][1000 genomes]
rs558126	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs558242	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs559565	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs559612	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs563424	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs563662	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs564361	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs565013	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs566320	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62386724	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62386725	0.80[ASN][1000 genomes]
rs821298	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs821299	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs821300	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357720	0.82[JPT][hapmap];0.80[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:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13376800-13395200	Weak transcription	NHEK	skin
3	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
4	chr6:13381800-13395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:13382400-13397600	Weak transcription	Esophagus	oesophagus
6	chr6:13383800-13395400	Weak transcription	Brain Anterior Caudate	brain
7	chr6:13384000-13395400	Weak transcription	Brain Substantia Nigra	brain
8	chr6:13384000-13395400	Weak transcription	NHLF	lung
9	chr6:13384200-13395200	Weak transcription	Adipose Nuclei	Adipose
10	chr6:13384200-13395400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:13384200-13395400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:13384200-13395400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:13384600-13395400	Weak transcription	Primary B cells from cord blood	blood
14	chr6:13385000-13393200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:13385600-13393000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:13385800-13392200	Weak transcription	Right Ventricle	heart
17	chr6:13386800-13392800	Weak transcription	Fetal Heart	heart
18	chr6:13387000-13392200	Weak transcription	Left Ventricle	heart
19	chr6:13387000-13395400	Weak transcription	Lung	lung
20	chr6:13387000-13395400	Weak transcription	Right Atrium	heart
21	chr6:13387000-13396000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:13387200-13393000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:13387400-13395400	Weak transcription	Psoas Muscle	Psoas
24	chr6:13390200-13393000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:13390400-13395400	Weak transcription	Pancreas	Pancrea
26	chr6:13390800-13392400	Enhancers	Primary B cells from peripheral blood	blood
27	chr6:13391000-13392200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr6:13391200-13392800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:13391200-13393200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:13391400-13392200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:13391400-13394400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:13391400-13395000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr6:13391400-13395200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:13391400-13395400	Weak transcription	Spleen	Spleen
35	chr6:13391600-13392800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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