Variant report

Variant	rs2275710
Chromosome Location	chr9:100935050-100935051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100932527..100936703-chr9:100952110..100957364,6	MCF-7	breast:
2	chr9:100934229..100937131-chr9:101015572..101018332,2	MCF-7	breast:
3	chr9:100934419..100936711-chr9:100950978..100955014,5	MCF-7	breast:
4	chr9:100934290..100936965-chr9:101016512..101018556,3	K562	blood:

Variant related genes	Relation type
ENSG00000106789	Chromatin interaction
ENSG00000095383	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10491723	0.83[EUR][1000 genomes]
rs10818543	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12551204	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1539289	0.96[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2231652	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2231656	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3758263	0.80[ASN][1000 genomes]
rs56735263	0.80[ASN][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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv893613	chr9:100885779-100943397	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2275710	TBC1D2	cis	cerebellum	SCAN
rs2275710	TGFBR1	cis	cerebellum	SCAN
rs2275710	TBC1D2	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100920400-100942200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:100921800-100935200	Weak transcription	Lung	lung
3	chr9:100924600-100939000	Enhancers	Duodenum Mucosa	Duodenum
4	chr9:100927000-100936800	Weak transcription	Thymus	Thymus
5	chr9:100929800-100935800	Enhancers	K562	blood
6	chr9:100930800-100936000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:100930800-100938000	Genic enhancers	Fetal Intestine Small	intestine
8	chr9:100931400-100937400	Weak transcription	Spleen	Spleen
9	chr9:100931800-100954400	Weak transcription	Right Atrium	heart
10	chr9:100932000-100937400	Weak transcription	Primary B cells from cord blood	blood
11	chr9:100932000-100937400	Enhancers	HepG2	liver
12	chr9:100932200-100937600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:100932400-100937400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:100932400-100937600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:100932600-100937200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr9:100932800-100936200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr9:100932800-100951200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:100933000-100936400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:100933200-100935600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:100933400-100935400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:100933400-100935400	Enhancers	Fetal Thymus	thymus
22	chr9:100933400-100935600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:100933400-100935800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr9:100933400-100936000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:100933400-100951400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:100933600-100935200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:100933600-100935200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr9:100933600-100935400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr9:100933600-100935600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr9:100933600-100935800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr9:100933600-100936000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr9:100933600-100942600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:100933800-100937600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr9:100933800-100942400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr9:100933800-100950200	Weak transcription	Colonic Mucosa	Colon
36	chr9:100933800-100951400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:100934000-100935400	Enhancers	NHEK	skin
38	chr9:100934200-100935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:100934200-100935200	Weak transcription	Gastric	stomach
40	chr9:100934400-100936000	Enhancers	Stomach Mucosa	stomach
41	chr9:100934400-100954000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr9:100934600-100937000	Enhancers	Small Intestine	intestine
43	chr9:100934800-100935200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:100934800-100935200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:100934800-100935200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr9:100934800-100935200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:100934800-100935400	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr9:100934800-100935600	Enhancers	Hela-S3	cervix
49	chr9:100934800-100936000	Enhancers	Liver	Liver
50	chr9:100935000-100935200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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