Variant report

Variant	rs16932062
Chromosome Location	chr9:117776052-117776053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:117443499..117444975-chr9:117775722..117777924,20	MCF-7	breast:
2	chr9:117672786..117673783-chr9:117775999..117776990,4	MCF-7	breast:
3	chr9:117443479..117444428-chr9:117776016..117776531,2	K562	blood:
4	chr9:117502244..117504474-chr9:117775999..117777643,2	MCF-7	breast:
5	chr9:117500446..117501896-chr9:117775969..117778215,11	MCF-7	breast:
6	chr9:117713895..117715040-chr9:117775983..117776889,3	MCF-7	breast:
7	chr9:117442900..117446108-chr9:117775232..117777695,3	MCF-7	breast:
8	chr9:117660650..117663296-chr9:117774626..117776386,2	MCF-7	breast:
9	chr9:117676108..117677078-chr9:117776037..117776911,10	MCF-7	breast:
10	chr9:117500847..117501439-chr9:117776002..117776751,3	K562	blood:
11	chr9:117443095..117445141-chr9:117775959..117778088,21	MCF-7	breast:
12	chr14:107158122..107158971-chr9:117776020..117776679,2	MCF-7	breast:

No data

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1107372	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11793430	0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11794797	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1330365	0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1999223	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236409	0.82[JPT][hapmap]
rs62578742	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7851618	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs944225	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16932062	TBX1	trans	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117771200-117783000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:117771400-117776200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr9:117771400-117778600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:117771400-117784600	Weak transcription	HMEC	breast
5	chr9:117771800-117779000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
7	chr9:117773600-117787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:117773800-117776600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:117774200-117776200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:117774400-117780400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:117774800-117783200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:117775000-117782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:117775200-117777000	Enhancers	Dnd41	blood
14	chr9:117775600-117780400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:117775800-117776200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:117775800-117776800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:117775800-117776800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr9:117775800-117776800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:117776000-117776200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:117776000-117776200	Enhancers	Fetal Lung	lung
21	chr9:117776000-117776200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr9:117776000-117776400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:117776000-117776400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr9:117776000-117776400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:117776000-117776400	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr9:117776000-117776600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr9:117776000-117776800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr9:117776000-117776800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr9:117776000-117776800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr9:117776000-117776800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr9:117776000-117776800	Enhancers	Hela-S3	cervix

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