Variant report

Variant	rs6938843
Chromosome Location	chr6:45544829-45544830
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr6:45544533-45544976	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr6:45544551-45545055	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr6:45544805-45544932	MCF-7	breast:	n/a	n/a
4	ESR1	chr6:45544565-45545037	ECC-1	luminal epithelium:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUPT3H-1	chr6:45544796-45545334	XLOC_005737
2	lnc-RUNX2-1	chr6:45543599-45545853	XLOC_005302

Variant related genes	Relation type
ENSG00000261080	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10807322	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10948242	0.88[ASN][1000 genomes]
rs11751172	0.88[ASN][1000 genomes]
rs11751184	0.88[ASN][1000 genomes]
rs12201995	0.98[ASN][1000 genomes]
rs12202314	0.83[EUR][1000 genomes]
rs12204264	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13200687	0.88[ASN][1000 genomes]
rs13205082	0.88[ASN][1000 genomes]
rs1928529	0.82[ASN][1000 genomes]
rs2280225	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280228	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2280229	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34528484	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35611098	0.98[ASN][1000 genomes]
rs68057028	0.98[ASN][1000 genomes]
rs6913882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6914235	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937759	0.97[ASN][1000 genomes]
rs6938170	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938214	0.98[ASN][1000 genomes]
rs6938450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463100	0.84[ASN][1000 genomes]
rs9463102	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463103	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9472507	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472508	0.98[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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv462940	chr6:45532214-45545975	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv603010	chr6:45532214-45545975	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr6:45537400-45559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:45537600-45545200	Weak transcription	NH-A	brain
3	chr6:45537600-45546000	Weak transcription	Right Atrium	heart
4	chr6:45542800-45554000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:45543800-45545600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:45544400-45545000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:45544400-45545000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:45544400-45545400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:45544600-45545000	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr6:45544600-45545000	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr6:45544600-45545000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
12	chr6:45544600-45545000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr6:45544600-45545000	Enhancers	Left Ventricle	heart
14	chr6:45544600-45545000	Enhancers	Right Ventricle	heart
15	chr6:45544600-45545200	Flanking Active TSS	Brain Substantia Nigra	brain
16	chr6:45544600-45545400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:45544600-45545400	Enhancers	Lung	lung
18	chr6:45544600-45545800	Enhancers	Fetal Heart	heart
19	chr6:45544600-45546200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:45544600-45546400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:45544800-45545000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:45544800-45545000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:45544800-45545000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:45544800-45545000	Enhancers	Fetal Muscle Leg	muscle
25	chr6:45544800-45545200	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr6:45544800-45545400	Enhancers	Ovary	ovary
27	chr6:45544800-45545400	Enhancers	NHDF-Ad	bronchial
28	chr6:45544800-45545600	Enhancers	Brain Angular Gyrus	brain
29	chr6:45544800-45546000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:45544800-45546000	Enhancers	Brain Germinal Matrix	brain
31	chr6:45544800-45546200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:45544800-45546200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:45544800-45546200	Enhancers	Fetal Stomach	stomach
34	chr6:45544800-45546200	Enhancers	HSMM	muscle
35	chr6:45544800-45546200	Enhancers	HSMMtube	muscle
36	chr6:45544800-45546200	Enhancers	NHLF	lung
37	chr6:45544800-45546600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:45544800-45546600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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