Variant report

Variant	rs11159290
Chromosome Location	chr14:78289694-78289695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78269397..78271453-chr14:78289633..78292223,2	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10130790	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10141465	0.84[ASN][1000 genomes]
rs10146144	0.83[ASN][1000 genomes]
rs10873312	0.86[EUR][1000 genomes]
rs1107991	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11159291	0.83[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11159294	0.83[CHB][hapmap]
rs11159298	0.87[CHB][hapmap]
rs11159300	0.87[CHB][hapmap]
rs11159301	0.87[CHB][hapmap]
rs11159302	0.86[CHB][hapmap]
rs11159306	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11622297	0.82[CHB][hapmap]
rs11628049	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12587361	0.87[CHB][hapmap]
rs12878904	0.87[CHB][hapmap]
rs12879726	0.83[CHB][hapmap]
rs12884153	0.83[CHB][hapmap]
rs12893815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12894510	0.84[CEU][hapmap]
rs2003600	0.87[CHB][hapmap]
rs2010591	0.82[CHB][hapmap]
rs2017927	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2052444	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2080814	0.95[ASN][1000 genomes]
rs2080815	0.87[CHB][hapmap]
rs2080816	0.87[CHB][hapmap]
rs2080817	0.87[CHB][hapmap]
rs2098583	0.92[ASN][1000 genomes]
rs2098584	0.90[CHB][hapmap]
rs2112129	0.85[ASN][1000 genomes]
rs2287648	0.87[CHB][hapmap]
rs2364739	0.94[ASN][1000 genomes]
rs2364741	0.95[ASN][1000 genomes]
rs2364743	0.87[CHB][hapmap]
rs2364744	0.81[ASN][1000 genomes]
rs2364745	0.84[ASN][1000 genomes]
rs2364842	0.83[CHB][hapmap]
rs2886167	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2886168	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3783962	0.87[CHB][hapmap]
rs3783966	0.87[CHB][hapmap]
rs3783968	0.87[CHB][hapmap]
rs3783969	0.82[CHB][hapmap]
rs3783971	0.82[ASN][1000 genomes]
rs3783974	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs3825691	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3825692	0.94[ASN][1000 genomes]
rs4359362	0.83[CHB][hapmap]
rs4371094	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4393507	0.83[CHB][hapmap]
rs4448861	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4899677	0.83[CHB][hapmap];0.85[LWK][hapmap]
rs4899678	0.87[CHB][hapmap]
rs4899679	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4903650	0.86[EUR][1000 genomes]
rs4903652	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4903653	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4903654	0.83[CHB][hapmap]
rs4903655	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs4903656	0.87[CHB][hapmap]
rs4903658	0.87[CHB][hapmap]
rs4903660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4903661	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4903662	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4903663	0.87[CHB][hapmap]
rs4903664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6574406	0.84[ASN][1000 genomes]
rs6574408	0.83[ASN][1000 genomes]
rs7145309	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7146020	0.82[CHB][hapmap]
rs7149884	0.87[CHB][hapmap]
rs7149911	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs7151404	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs719049	0.83[CHB][hapmap]
rs724263	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs726538	0.83[CHB][hapmap]
rs7401295	0.86[EUR][1000 genomes]
rs741573	0.87[CHB][hapmap]
rs741574	0.87[CHB][hapmap]
rs741575	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7493386	0.85[CHB][hapmap]
rs8004053	0.90[ASN][1000 genomes]
rs8006218	0.86[ASN][1000 genomes]
rs8009433	0.87[CHB][hapmap]
rs8009937	0.89[ASN][1000 genomes]
rs8010212	0.86[ASN][1000 genomes]
rs8014296	0.87[CHB][hapmap]
rs8018674	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8019539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8022985	0.90[ASN][1000 genomes]
rs874025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs877561	0.86[CHB][hapmap]
rs962539	0.91[CHB][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11159290	NRXN3	cis	cerebellum	SCAN
rs11159290	FAM181B	trans	parietal	SCAN
rs11159290	ADCK1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78267200-78304200	Weak transcription	HSMMtube	muscle
2	chr14:78267200-78310800	Weak transcription	Esophagus	oesophagus
3	chr14:78274800-78316600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:78283000-78293400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr14:78283200-78301800	Weak transcription	Small Intestine	intestine
6	chr14:78283600-78311000	Weak transcription	Hela-S3	cervix
7	chr14:78283800-78297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:78284000-78292200	Weak transcription	Stomach Mucosa	stomach
9	chr14:78284000-78299400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr14:78284200-78298000	Weak transcription	HepG2	liver
11	chr14:78284200-78309400	Weak transcription	Brain Germinal Matrix	brain
12	chr14:78284200-78312600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr14:78284800-78289800	Strong transcription	Fetal Muscle Leg	muscle
14	chr14:78284800-78291600	Weak transcription	Fetal Heart	heart
15	chr14:78284800-78300800	Weak transcription	Fetal Brain Male	brain
16	chr14:78284800-78305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr14:78285200-78290200	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr14:78285200-78293200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr14:78285400-78289800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:78285800-78305800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr14:78286200-78299000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr14:78286200-78301800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr14:78286200-78303000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:78286400-78293400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr14:78286400-78294000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:78286400-78299200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr14:78286400-78300400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr14:78286400-78303000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr14:78286400-78305200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr14:78286600-78292200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr14:78287000-78290600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr14:78287000-78292200	Weak transcription	Gastric	stomach
33	chr14:78287000-78297400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr14:78287000-78301400	Weak transcription	Right Ventricle	heart
35	chr14:78287000-78309400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr14:78287000-78309600	Weak transcription	Osteobl	bone
37	chr14:78288000-78289800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr14:78288200-78289800	Strong transcription	Fetal Brain Female	brain
39	chr14:78288400-78289800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr14:78288400-78290000	Strong transcription	Thymus	Thymus
41	chr14:78288400-78290400	Strong transcription	Fetal Intestine Small	intestine
42	chr14:78288600-78289800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr14:78288600-78289800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr14:78288600-78289800	Strong transcription	Placenta	Placenta
45	chr14:78288600-78289800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr14:78288600-78290200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr14:78288600-78290200	Strong transcription	Colon Smooth Muscle	Colon
48	chr14:78288600-78290400	Strong transcription	Fetal Intestine Large	intestine
49	chr14:78288600-78290800	Weak transcription	Fetal Lung	lung
50	chr14:78288600-78290800	Strong transcription	Fetal Stomach	stomach

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