Variant report

Variant	rs17102309
Chromosome Location	chr1:79306199-79306200
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:79299275..79301209-chr1:79305174..79307511,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10518590	0.80[EUR][1000 genomes]
rs17102289	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17102292	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17102312	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17102367	0.82[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs17401994	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2996692	0.95[EUR][1000 genomes]
rs57388815	0.95[EUR][1000 genomes]
rs6424614	0.90[EUR][1000 genomes]
rs6667376	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6682731	0.95[EUR][1000 genomes]
rs6690213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7516845	0.80[EUR][1000 genomes]
rs7525345	0.82[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs7528069	0.80[EUR][1000 genomes]
rs7531816	0.92[EUR][1000 genomes]
rs7535891	0.95[EUR][1000 genomes]
rs7543576	0.95[EUR][1000 genomes]
rs7543883	0.95[EUR][1000 genomes]
rs7549910	0.95[EUR][1000 genomes]
rs984361	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs984656	0.80[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
rs17102309	TBX1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79302800-79306200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:79302800-79306200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:79303000-79306200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:79305600-79306200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:79305600-79306200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:79305600-79306200	Enhancers	Fetal Lung	lung
7	chr1:79305600-79306200	Enhancers	HSMM	muscle
8	chr1:79305600-79306200	Enhancers	NHDF-Ad	bronchial
9	chr1:79305600-79306200	Enhancers	Osteobl	bone
10	chr1:79305600-79306400	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr1:79305600-79307400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:79305800-79306200	Enhancers	Liver	Liver
13	chr1:79305800-79306200	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr1:79305800-79306200	Enhancers	NH-A	brain
15	chr1:79305800-79306400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:79305800-79306600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:79305800-79307600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:79306000-79306200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:79306000-79306200	Active TSS	Brain Hippocampus Middle	brain
20	chr1:79306000-79306200	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:79306000-79306200	Enhancers	NHLF	lung
22	chr1:79306000-79306400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:79306000-79306600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:79306000-79306800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:79306000-79306800	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:79306000-79306800	Enhancers	Brain Germinal Matrix	brain
27	chr1:79306000-79307000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:79306000-79307000	Enhancers	Adipose Nuclei	Adipose
29	chr1:79306000-79307000	Enhancers	Hela-S3	cervix
30	chr1:79306000-79307200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:79306000-79307200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:79306000-79307200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:79306000-79309600	Enhancers	Fetal Stomach	stomach

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