Variant report

Variant	rs4743176
Chromosome Location	chr9:100930659-100930660
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100929714..100931731-chr9:100933494..100935958,2	K562	blood:
2	chr9:100927949..100931625-chr9:100946011..100949394,3	K562	blood:
3	chr9:100930069..100933063-chr9:100933663..100936506,3	MCF-7	breast:
4	chr9:100921877..100926007-chr9:100929067..100934621,5	K562	blood:
5	chr9:100881024..100882919-chr9:100930055..100932510,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106785	Chromatin interaction
ENSG00000106789	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10818534	0.83[ASN][1000 genomes]
rs12550850	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290961	0.91[ASN][1000 genomes]
rs1539288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539289	0.92[LWK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs1891322	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.91[ASN][1000 genomes]
rs4743174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743175	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478581	0.86[ASN][1000 genomes]
rs72603681	0.99[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
rs4743176	C9orf102	cis	cerebellum	SCAN
rs4743176	TBC1D2	cis	parietal	SCAN
rs4743176	CORO2A	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100889200-100930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:100891000-100930800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:100896000-100931000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:100898400-100931200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:100909200-100930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:100909400-100933600	Weak transcription	Colonic Mucosa	Colon
7	chr9:100914600-100931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:100917600-100933400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:100919400-100930800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:100919600-100932200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr9:100920000-100931000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:100920400-100942200	Weak transcription	Primary T cells from cord blood	blood
13	chr9:100921800-100935200	Weak transcription	Lung	lung
14	chr9:100922400-100933600	Weak transcription	Gastric	stomach
15	chr9:100924600-100939000	Enhancers	Duodenum Mucosa	Duodenum
16	chr9:100924800-100931600	Weak transcription	Right Atrium	heart
17	chr9:100924800-100935000	Enhancers	Fetal Intestine Large	intestine
18	chr9:100925200-100930800	Weak transcription	Spleen	Spleen
19	chr9:100925200-100931200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr9:100926200-100932000	Weak transcription	Esophagus	oesophagus
21	chr9:100926200-100935000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:100926800-100934800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:100927000-100930800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr9:100927000-100936800	Weak transcription	Thymus	Thymus
25	chr9:100927200-100930800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr9:100927200-100930800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:100927200-100930800	Weak transcription	NHEK	skin
28	chr9:100927200-100931200	Weak transcription	Fetal Thymus	thymus
29	chr9:100927600-100930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:100927600-100930800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr9:100927600-100930800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:100928000-100930800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:100928000-100930800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:100928200-100930800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr9:100928200-100933000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr9:100929000-100932600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr9:100929200-100931000	Weak transcription	Small Intestine	intestine
38	chr9:100929600-100930800	Enhancers	Fetal Intestine Small	intestine
39	chr9:100929800-100932400	Enhancers	Stomach Mucosa	stomach
40	chr9:100929800-100935800	Enhancers	K562	blood
41	chr9:100930000-100930800	Weak transcription	Primary B cells from cord blood	blood
42	chr9:100930200-100932800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:100930400-100931000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr9:100930400-100931200	Enhancers	HepG2	liver
45	chr9:100930400-100932400	Enhancers	HMEC	breast
46	chr9:100930400-100933800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:100930600-100931000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:100930600-100932200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr9:100930600-100932200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr9:100930600-100932200	Enhancers	Rectal Mucosa Donor 31	rectum

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