Variant report

Variant	rs17102312
Chromosome Location	chr1:79307988-79307989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10518590	0.85[EUR][1000 genomes]
rs17102289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17102309	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17102367	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs17401994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2996692	1.00[EUR][1000 genomes]
rs41312730	0.80[EUR][1000 genomes]
rs57388815	1.00[EUR][1000 genomes]
rs6424614	0.95[EUR][1000 genomes]
rs6667376	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6682731	1.00[EUR][1000 genomes]
rs6690213	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7516845	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7525345	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7528069	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7531816	0.97[EUR][1000 genomes]
rs7535891	1.00[EUR][1000 genomes]
rs7543576	1.00[EUR][1000 genomes]
rs7543883	1.00[EUR][1000 genomes]
rs7549910	1.00[EUR][1000 genomes]
rs984361	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs984656	0.80[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv526221	chr1:79197624-79487080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv817535	chr1:79203834-79473089	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999624	chr1:79230028-79448222	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535013	chr1:79230028-79448222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546619	chr1:79233493-79614989	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1000656	chr1:79303750-79337233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1003295	chr1:79303750-79344930	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17102312	TBX1	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79306000-79309600	Enhancers	Fetal Stomach	stomach
2	chr1:79307000-79308000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:79307000-79308400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:79307000-79309600	Enhancers	HSMMtube	muscle
5	chr1:79307200-79308000	Weak transcription	Fetal Lung	lung
6	chr1:79307200-79308200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:79307200-79308200	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:79307200-79309400	Enhancers	Osteobl	bone
9	chr1:79307200-79309800	Enhancers	NH-A	brain
10	chr1:79307200-79310200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:79307200-79310200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:79307400-79309000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:79307400-79317200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:79307600-79308400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:79307600-79308800	Weak transcription	NHDF-Ad	bronchial
16	chr1:79307600-79309000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:79307600-79309400	Weak transcription	Fetal Kidney	kidney

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