Variant report

Variant	rs3798499
Chromosome Location	chr6:100864829-100864830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100858630..100860208-chr6:100863468..100866300,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11155437	0.84[EUR][1000 genomes]
rs12662778	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13211871	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs1395119	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs1472799	0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1506081	0.85[EUR][1000 genomes]
rs1506084	0.84[EUR][1000 genomes]
rs1546393	0.95[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17060530	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1876156	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1876157	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2032511	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2202537	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs34501046	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3734357	0.91[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778037	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3778038	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs3778040	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs3798509	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4839779	0.86[EUR][1000 genomes]
rs4840129	0.85[EUR][1000 genomes]
rs7747929	0.91[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868568	0.81[EUR][1000 genomes]
rs9390335	0.85[EUR][1000 genomes]
rs9390345	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9399560	0.85[EUR][1000 genomes]
rs9403721	0.84[EUR][1000 genomes]
rs9403723	0.85[EUR][1000 genomes]
rs9403728	0.85[EUR][1000 genomes]
rs9403740	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.82[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	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

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100831200-100874000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:100838400-100874800	Weak transcription	Psoas Muscle	Psoas
3	chr6:100839400-100874200	Weak transcription	HSMM	muscle
4	chr6:100842000-100866400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:100852200-100871200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:100856800-100874800	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:100862200-100890600	Weak transcription	Adipose Nuclei	Adipose
8	chr6:100862800-100865200	Enhancers	Dnd41	blood
9	chr6:100862800-100865600	Enhancers	Fetal Intestine Large	intestine
10	chr6:100863000-100894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:100863800-100868000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:100863800-100868000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:100864000-100868200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:100864000-100887000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:100864200-100867600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:100864200-100870400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:100864400-100869600	Weak transcription	Fetal Intestine Small	intestine

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