Variant report

Variant	rs6808242
Chromosome Location	chr3:100550136-100550137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100548174..100550868-chr3:100558389..100562132,3	K562	blood:

Variant related genes	Relation type
ENSG00000154175	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12696195	0.83[TSI][hapmap]
rs13069634	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13433770	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs1992107	0.90[EUR][1000 genomes]
rs59590198	0.91[ASN][1000 genomes]
rs6765500	0.87[CEU][hapmap]
rs7615467	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7652397	0.84[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9814084	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs9833369	0.92[EUR][1000 genomes]
rs9845149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9873555	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs9877253	0.93[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877221	chr3:100546974-100592709	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6808242	GPR128	cis	multi-tissue	Pritchard
rs6808242	FAM55C	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100505200-100558200	Weak transcription	Ovary	ovary
2	chr3:100505200-100582800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:100516000-100572200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:100517400-100594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:100530000-100594400	Weak transcription	HSMM	muscle
6	chr3:100530800-100555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:100531600-100555400	Weak transcription	NHDF-Ad	bronchial
8	chr3:100533800-100573000	Weak transcription	Aorta	Aorta
9	chr3:100539000-100558200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:100545600-100554400	Strong transcription	Osteobl	bone
11	chr3:100547000-100553800	Strong transcription	HSMMtube	muscle
12	chr3:100547000-100555600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:100547600-100550600	Strong transcription	Fetal Muscle Leg	muscle
14	chr3:100547600-100553800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:100548400-100552400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:100548600-100555400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:100548600-100558200	Weak transcription	Fetal Stomach	stomach
18	chr3:100549400-100563000	Weak transcription	Fetal Lung	lung
19	chr3:100549800-100562200	Weak transcription	Fetal Intestine Large	intestine
20	chr3:100550000-100550200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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