Variant report

Variant	rs1469800
Chromosome Location	chr9:101026042-101026043
allele	A/G
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100978261..100978893-chr9:101025777..101026288,2	MCF-7	breast:
2	chr9:101017313..101019971-chr9:101024791..101026920,2	MCF-7	breast:
3	chr9:100967700..100968256-chr9:101025763..101027217,6	MCF-7	breast:
4	chr9:100880329..100883206-chr9:101025996..101028168,2	MCF-7	breast:
5	chr9:100986971..100987476-chr9:101025923..101026674,2	K562	blood:
6	chr9:100930862..100931822-chr9:101025607..101026459,2	K562	blood:
7	chr9:100978228..100978771-chr9:101025810..101026449,2	MCF-7	breast:
8	chr9:100836404..100837181-chr9:101025639..101026636,4	K562	blood:
9	chr9:100967687..100968926-chr9:101025676..101026669,6	K562	blood:
10	chr9:100954115..100956214-chr9:101024702..101026397,2	MCF-7	breast:
11	chr9:101010177..101013807-chr9:101023006..101027119,4	K562	blood:
12	chr9:100684316..100685157-chr9:101025719..101026655,2	NB4	blood:
13	chr9:100944487..100947115-chr9:101025463..101028083,2	MCF-7	breast:
14	chr9:100967704..100968857-chr9:101025808..101026669,3	MCF-7	breast:
15	chr9:100836667..100837319-chr9:101025705..101026458,2	MCF-7	breast:
16	chr9:100685496..100686599-chr9:101025791..101026677,7	MCF-7	breast:
17	chr9:100836374..100837282-chr9:101025777..101026312,2	MCF-7	breast:
18	chr9:100966646..100969743-chr9:101023259..101026194,3	K562	blood:
19	chr9:101017245..101019908-chr9:101024974..101027737,3	MCF-7	breast:
20	chr9:100955096..100955755-chr9:101025700..101026542,2	MCF-7	breast:
21	chr9:100818347..100819097-chr9:101025427..101026319,2	MCF-7	breast:
22	chr9:100685710..100686367-chr9:101025985..101026665,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000106789	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000106785	Chromatin interaction
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10818669	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10985441	0.81[AMR][1000 genomes]
rs10985666	0.96[ASN][1000 genomes]
rs12343641	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435261	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469802	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023361	0.81[AMR][1000 genomes]
rs2417893	0.84[AMR][1000 genomes]
rs2900463	0.84[AMR][1000 genomes]
rs3739664	0.84[AMR][1000 genomes]
rs3780450	0.81[AMR][1000 genomes]
rs4743186	0.84[AMR][1000 genomes]
rs4743193	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7021760	0.84[AMR][1000 genomes]
rs733040	0.83[AMR][1000 genomes]
rs7850360	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7855855	0.86[AMR][1000 genomes]
rs942166	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv519818	chr9:101024887-101092316	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1469800	TBC1D2	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101019600-101026200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:101019600-101027200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr9:101023600-101026200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:101024000-101026400	Enhancers	HSMMtube	muscle
5	chr9:101024400-101026200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:101024400-101026200	Enhancers	HSMM	muscle
7	chr9:101024800-101027600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:101025400-101026200	Enhancers	Osteobl	bone
9	chr9:101025400-101028400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr9:101025600-101027000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:101025800-101026200	Weak transcription	K562	blood
12	chr9:101025800-101026800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr9:101026000-101026200	Enhancers	NHDF-Ad	bronchial

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