Variant report

Variant	rs10991680
Chromosome Location	chr9:108277423-108277424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:108277381-108277567	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RALGAPA1P	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1018848	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1018849	0.89[ASN][1000 genomes]
rs1024366	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10820805	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10820806	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10820807	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10820808	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10820816	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10991661	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10991662	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10991664	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10991666	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10991669	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10991675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10991686	0.81[AMR][1000 genomes]
rs10991688	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11525961	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11535511	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12235779	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12555267	0.91[ASN][1000 genomes]
rs1327351	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1329021	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1329022	0.92[ASN][1000 genomes]
rs1576285	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16924672	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16924676	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858744	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1928293	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1928294	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2010861	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2068266	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2518109	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2518110	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2518111	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2518113	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2518117	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2518118	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2518119	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518122	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518127	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2518132	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2518133	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2768278	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2768282	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2768284	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2768285	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2768286	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2768287	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2768288	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2768293	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2768295	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2768296	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2904847	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4302902	0.92[ASN][1000 genomes]
rs56134629	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72744254	0.81[ASN][1000 genomes]
rs72744266	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72744269	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs879115	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs879117	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs879118	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs885955	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
3	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
6	chr9:108258200-108282000	Weak transcription	Psoas Muscle	Psoas
7	chr9:108259600-108282000	Weak transcription	HSMMtube	muscle
8	chr9:108262800-108277600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:108266400-108277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:108266600-108278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:108266600-108278000	Weak transcription	K562	blood
12	chr9:108266600-108282000	Weak transcription	Hela-S3	cervix
13	chr9:108266800-108277800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:108268200-108279000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:108268200-108279600	Weak transcription	Fetal Kidney	kidney
16	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
17	chr9:108269200-108282000	Weak transcription	Pancreas	Pancrea
18	chr9:108269400-108280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:108269800-108282000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:108269800-108286200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:108270800-108280200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:108271200-108280200	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:108272600-108282000	Weak transcription	Gastric	stomach
24	chr9:108272800-108282400	Weak transcription	NHLF	lung
25	chr9:108272800-108304600	Weak transcription	NHEK	skin
26	chr9:108273000-108277600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:108273000-108282000	Weak transcription	HSMM	muscle
28	chr9:108273000-108282000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr9:108273000-108282200	Weak transcription	NH-A	brain
30	chr9:108273000-108282200	Weak transcription	NHDF-Ad	bronchial
31	chr9:108273600-108277600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr9:108274200-108278000	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:108274200-108278200	Weak transcription	Brain Substantia Nigra	brain
34	chr9:108274200-108279400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:108274400-108277800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
37	chr9:108275200-108278000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:108275200-108279000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:108275200-108282000	Weak transcription	Esophagus	oesophagus
40	chr9:108275400-108279000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:108275400-108279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:108276000-108279200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:108276000-108282000	Weak transcription	Osteobl	bone
44	chr9:108276200-108277800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:108276200-108278800	ZNF genes & repeats	GM12878-XiMat	blood
46	chr9:108276200-108309200	Weak transcription	Lung	lung
47	chr9:108276400-108282000	Weak transcription	Spleen	Spleen
48	chr9:108276600-108279600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:108276800-108277600	Strong transcription	Dnd41	blood
50	chr9:108276800-108278000	Strong transcription	Rectal Smooth Muscle	rectum

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