Variant report

Variant	rs477973
Chromosome Location	chr6:11540590-11540591
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11537155..11540056-chr6:11540130..11543939,4	MCF-7	breast:
2	chr6:11539069..11540912-chr6:11545787..11548453,2	K562	blood:

Variant related genes	Relation type
ENSG00000205269	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10046197	1.00[EUR][1000 genomes]
rs1150563	1.00[EUR][1000 genomes]
rs1150569	1.00[EUR][1000 genomes]
rs1195651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11962713	1.00[EUR][1000 genomes]
rs12332876	1.00[EUR][1000 genomes]
rs2807965	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295057	1.00[EUR][1000 genomes]
rs544766	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs552548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs585322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58716971	1.00[EUR][1000 genomes]
rs59791855	1.00[EUR][1000 genomes]
rs609389	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs613353	1.00[EUR][1000 genomes]
rs61378967	1.00[EUR][1000 genomes]
rs61679516	1.00[EUR][1000 genomes]
rs617146	1.00[EUR][1000 genomes]
rs656674	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6936918	1.00[EUR][1000 genomes]
rs6940009	1.00[EUR][1000 genomes]
rs73351939	1.00[EUR][1000 genomes]
rs73351942	1.00[EUR][1000 genomes]
rs73351967	1.00[EUR][1000 genomes]
rs73351970	1.00[EUR][1000 genomes]
rs73351978	1.00[EUR][1000 genomes]
rs73351980	1.00[EUR][1000 genomes]
rs73355853	1.00[EUR][1000 genomes]
rs73368833	1.00[EUR][1000 genomes]
rs7744252	1.00[EUR][1000 genomes]
rs7744403	1.00[EUR][1000 genomes]
rs7761428	1.00[EUR][1000 genomes]
rs821537	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs821541	0.83[AMR][1000 genomes];1.00[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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11537000-11540600	Active TSS	Brain Angular Gyrus	brain
2	chr6:11537400-11543200	Active TSS	GM12878-XiMat	blood
3	chr6:11539000-11540600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:11539400-11540600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:11539600-11547000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:11539800-11541600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr6:11540000-11540600	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:11540000-11540600	Weak transcription	Brain Substantia Nigra	brain
9	chr6:11540000-11541000	Enhancers	Brain Anterior Caudate	brain
10	chr6:11540000-11541000	Enhancers	HepG2	liver
11	chr6:11540000-11541400	Enhancers	Fetal Brain Female	brain
12	chr6:11540000-11542200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:11540200-11540600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr6:11540200-11540600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:11540200-11540800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:11540200-11540800	Enhancers	Dnd41	blood
17	chr6:11540200-11542000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr6:11540200-11545400	Weak transcription	Fetal Brain Male	brain
19	chr6:11540200-11547000	Weak transcription	Adipose Nuclei	Adipose
20	chr6:11540200-11547000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:11540200-11552000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:11540400-11540600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:11540400-11540600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:11540400-11542800	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:11540400-11543200	Weak transcription	Primary B cells from cord blood	blood
26	chr6:11540400-11543800	Weak transcription	Liver	Liver
27	chr6:11540400-11544600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:11540400-11544800	Weak transcription	Brain Germinal Matrix	brain
29	chr6:11540400-11551600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr6:11540400-11552600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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