Variant report

Variant	rs740888
Chromosome Location	chr7:33541486-33541487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11769528	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13227256	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13438256	0.91[JPT][hapmap]
rs17170269	1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17170271	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs2041417	1.00[ASW][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2109526	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2392232	0.81[ASN][1000 genomes]
rs35822718	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779239	0.95[JPT][hapmap]
rs3823763	0.87[JPT][hapmap]
rs3884597	0.91[JPT][hapmap]
rs4604335	0.91[JPT][hapmap]
rs4723289	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6944723	0.91[JPT][hapmap]
rs71532578	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7798938	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs961679	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9639675	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9784973	0.91[JPT][hapmap]

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	nsv1016416	chr7:33241443-33559477	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830944	chr7:33389892-33549882	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv933237	chr7:33470390-33574046	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv933018	chr7:33506325-33707270	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830945	chr7:33526648-33670592	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs740888	BBS9	cis	parietal	SCAN
rs740888	BBS9	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33533800-33543800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:33534200-33552400	Weak transcription	Pancreas	Pancrea
3	chr7:33535200-33542000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:33535400-33547200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:33536400-33543600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:33536800-33546000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:33537000-33552200	Weak transcription	Aorta	Aorta
8	chr7:33538800-33541600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr7:33540000-33541600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:33540000-33541600	Enhancers	Psoas Muscle	Psoas
11	chr7:33540000-33544400	Enhancers	Fetal Muscle Leg	muscle
12	chr7:33540400-33543200	Enhancers	Brain Substantia Nigra	brain
13	chr7:33540600-33543200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:33540800-33541800	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:33540800-33543600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:33540800-33568600	Weak transcription	Left Ventricle	heart
17	chr7:33541200-33542000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr7:33541200-33543400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:33541200-33543800	Weak transcription	Fetal Stomach	stomach
20	chr7:33541200-33554600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:33541400-33542200	Weak transcription	HSMM	muscle
22	chr7:33541400-33543200	Weak transcription	Fetal Lung	lung
23	chr7:33541400-33567200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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