Variant report

Variant	rs3798497
Chromosome Location	chr6:100878858-100878859
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	chr6:100876201..100879163-chr6:100881481..100884143,2	K562	blood:
2	chr6:100854348..100856456-chr6:100877921..100879422,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1506080	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17060614	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17060615	0.88[ASN][1000 genomes]
rs1847912	0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1857859	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs241816	0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs3213541	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3734353	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3778030	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3778032	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3798488	0.87[ASN][1000 genomes]
rs3798490	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798492	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3798495	0.88[ASN][1000 genomes]
rs3830139	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs767933	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7741057	0.88[ASN][1000 genomes]
rs7757905	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv515895	chr6:100868779-100910798	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100862200-100890600	Weak transcription	Adipose Nuclei	Adipose
2	chr6:100863000-100894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:100864000-100887000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:100867400-100889000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:100869000-100882200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:100869400-100882200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:100874800-100880000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:100875000-100882200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:100875000-100882200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:100875200-100882000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:100875400-100880000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:100875400-100881800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:100875400-100882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:100875400-100890800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:100875600-100883800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:100875600-100891000	Weak transcription	HSMM	muscle
17	chr6:100875800-100879600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:100875800-100882000	Weak transcription	Psoas Muscle	Psoas
19	chr6:100875800-100882000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:100875800-100883200	Weak transcription	HSMMtube	muscle
21	chr6:100877600-100879000	Enhancers	Dnd41	blood
22	chr6:100878600-100879000	Flanking Active TSS	A549	lung
23	chr6:100878600-100879800	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr6:100878800-100879000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:100878800-100879000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:100878800-100879000	Enhancers	Pancreas	Pancrea
27	chr6:100878800-100879800	Enhancers	Gastric	stomach

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