Variant report

Variant	rs3763914
Chromosome Location	chr11:8940703-8940704
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8702949..8705431-chr11:8939246..8941790,2	K562	blood:
2	chr11:8940620..8943003-chr11:8946457..8949397,2	MCF-7	breast:
3	chr11:8932894..8935848-chr11:8939704..8942877,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166452	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10279	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769974	0.91[YRI][hapmap]
rs10840139	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10840151	0.87[YRI][hapmap]
rs10840154	0.87[YRI][hapmap]
rs11042105	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042106	0.90[ASW][hapmap];0.86[CEU][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11042108	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs11042114	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11042115	0.86[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042116	0.86[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042118	0.85[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042133	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11042148	0.95[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap]
rs1109304	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049908	0.86[CEU][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12223690	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs2163626	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs2248245	0.83[EUR][1000 genomes]
rs2455601	0.85[JPT][hapmap];0.84[MEX][hapmap]
rs2568068	0.87[EUR][1000 genomes]
rs2568070	0.87[EUR][1000 genomes]
rs2568085	1.00[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2568089	0.85[EUR][1000 genomes]
rs2568091	0.87[EUR][1000 genomes]
rs2568092	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2653569	0.82[TSI][hapmap]
rs2742484	0.83[EUR][1000 genomes]
rs2742485	0.82[EUR][1000 genomes]
rs3751063	0.87[YRI][hapmap]
rs3751064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751066	0.91[YRI][hapmap]
rs3763911	0.87[YRI][hapmap]
rs3763912	0.87[YRI][hapmap]
rs3763913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3815991	0.95[CHB][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs4909951	0.83[YRI][hapmap]
rs56680262	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59454329	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7104661	0.85[JPT][hapmap]
rs72632952	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7938995	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9300096	0.87[YRI][hapmap]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs3763914	TMEM9B-AS1	cis	Nerve Tibial	GTEx
rs3763914	TMEM9B-AS1	cis	Esophagus Mucosa	GTEx
rs3763914	ZNF143	cis	cerebellum	SCAN
rs3763914	TMEM9B-AS1	cis	Stomach	GTEx
rs3763914	NRIP3	cis	parietal	SCAN
rs3763914	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs3763914	EIF4G2	cis	cerebellum	SCAN
rs3763914	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs3763914	SYT9	cis	parietal	SCAN
rs3763914	TMEM9B-AS1	cis	lung	GTEx
rs3763914	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs3763914	TMEM9B-AS1	cis	Heart Left Ventricle	GTEx
rs3763914	DNHD1	cis	cerebellum	SCAN
rs3763914	TMEM9B-AS1	cis	Artery Tibial	GTEx
rs3763914	TMEM9B-AS1	cis	Thyroid	GTEx
rs3763914	MMP26	cis	cerebellum	SCAN
rs3763914	TMEM9B-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8933600-8944000	Weak transcription	Pancreas	Pancrea
3	chr11:8934000-8941800	Weak transcription	Colonic Mucosa	Colon
4	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:8934200-8941600	Weak transcription	Esophagus	oesophagus
6	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:8936000-8942800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:8936200-8945800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr11:8936400-8941800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:8936400-8946000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:8936400-8946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
13	chr11:8936600-8940800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:8936600-8941400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:8936600-8941600	Weak transcription	Ovary	ovary
16	chr11:8936600-8945000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:8936600-8945800	Weak transcription	Stomach Mucosa	stomach
18	chr11:8936600-8946600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
20	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
21	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:8936800-8942200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr11:8936800-8947000	Strong transcription	Dnd41	blood
24	chr11:8936800-8947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr11:8937000-8947600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:8937000-8948200	Strong transcription	Fetal Brain Female	brain
27	chr11:8937200-8945000	Strong transcription	Brain Angular Gyrus	brain
28	chr11:8937200-8947400	Strong transcription	Thymus	Thymus
29	chr11:8937600-8944800	Strong transcription	Hela-S3	cervix
30	chr11:8937800-8940800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:8937800-8947400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:8938000-8941200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr11:8938000-8941200	Strong transcription	K562	blood
34	chr11:8938000-8943000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:8938000-8943200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr11:8938000-8944200	Strong transcription	HUVEC	blood vessel
37	chr11:8938000-8944600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr11:8938000-8944800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:8938000-8944800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr11:8938000-8944800	Strong transcription	Fetal Intestine Large	intestine
41	chr11:8938000-8945000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr11:8938000-8945000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr11:8938000-8945800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:8938000-8946400	Strong transcription	Brain Hippocampus Middle	brain
45	chr11:8938000-8946600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:8938000-8946800	Strong transcription	Liver	Liver
47	chr11:8938000-8947400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr11:8938000-8947600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr11:8938200-8943000	Strong transcription	Primary hematopoietic stem cells	blood
50	chr11:8938200-8943200	Strong transcription	Primary T cells from cord blood	blood

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