Variant report

Variant	rs10121347
Chromosome Location	chr9:16806694-16806695
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10115109	0.82[EUR][1000 genomes]
rs10119731	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.84[EUR][1000 genomes]
rs10119811	0.84[EUR][1000 genomes]
rs10120562	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs10122901	0.88[CHB][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10122925	0.88[YRI][hapmap]
rs10125996	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10810635	0.89[CHB][hapmap];0.92[AMR][1000 genomes]
rs10962601	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10962609	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12338608	0.87[EUR][1000 genomes]
rs12341168	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12351269	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12376135	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12380481	0.82[EUR][1000 genomes]
rs16935073	0.84[ASW][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2183406	0.82[EUR][1000 genomes]
rs2183407	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2253579	0.88[CEU][hapmap]
rs4455968	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7861591	1.00[CEU][hapmap];0.93[EUR][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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10121347	BCAS3	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16796200-16810400	Weak transcription	HSMM	muscle
2	chr9:16796200-16813400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:16796200-16816800	Weak transcription	HSMMtube	muscle
4	chr9:16796400-16824400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:16796600-16809000	Weak transcription	Osteobl	bone
6	chr9:16798000-16809600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:16799200-16813200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:16802600-16807000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:16802800-16810000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:16802800-16811800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:16803200-16809200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:16803400-16809600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:16803800-16807000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:16803800-16811800	Weak transcription	NHLF	lung
15	chr9:16804000-16811800	Weak transcription	Fetal Stomach	stomach
16	chr9:16804000-16812000	Weak transcription	Ovary	ovary
17	chr9:16804600-16806800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:16804600-16806800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:16804600-16808800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr9:16804600-16809000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:16805600-16811000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr9:16806200-16806800	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:16806200-16807400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr9:16806200-16807800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:16806200-16807800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:16806200-16810000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:16806200-16810800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr9:16806400-16809400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:16806600-16807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:16806600-16810600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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