Variant report

Variant	rs11690687
Chromosome Location	chr2:98461821-98461822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10182941	0.86[CHB][hapmap]
rs10432626	0.85[EUR][1000 genomes]
rs11678558	0.91[CEU][hapmap]
rs11678591	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11679828	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11680018	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11680321	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11680883	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11681535	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684749	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11686881	0.91[CEU][hapmap];0.94[TSI][hapmap]
rs11687510	0.87[CEU][hapmap];0.94[TSI][hapmap]
rs11688829	1.00[CEU][hapmap];0.84[GIH][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11690737	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691494	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11692010	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11692470	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12052222	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12052836	0.84[EUR][1000 genomes]
rs12052846	0.85[EUR][1000 genomes]
rs12104810	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12712174	0.86[CHB][hapmap]
rs12988571	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12995673	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13004090	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13006932	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13008503	0.83[ASN][1000 genomes]
rs13008968	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13020776	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13023980	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13028954	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13032265	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13032883	0.85[EUR][1000 genomes]
rs13033383	0.91[CEU][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap]
rs13034929	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1317178	0.86[CHB][hapmap]
rs1470483	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17488834	0.91[CEU][hapmap]
rs17488897	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17489287	0.81[GIH][hapmap]
rs17489454	0.83[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17489915	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17489984	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17490429	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1838797	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1875699	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1922282	0.86[CHB][hapmap]
rs2044458	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2044459	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2084176	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2278700	0.91[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305143	0.91[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2309316	0.86[CHB][hapmap]
rs2871183	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3192177	0.91[CEU][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs3198055	0.82[EUR][1000 genomes]
rs34149969	0.84[EUR][1000 genomes]
rs34373359	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34502870	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34503448	0.84[EUR][1000 genomes]
rs34528940	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34654057	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34974566	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35098301	0.84[EUR][1000 genomes]
rs35218942	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35255677	0.85[EUR][1000 genomes]
rs35424768	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35505530	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35564270	0.83[EUR][1000 genomes]
rs35783535	0.85[EUR][1000 genomes]
rs4274643	0.86[CHB][hapmap]
rs4311104	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55776387	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55886305	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57681139	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58546246	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5865	0.86[CHB][hapmap]
rs62156511	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6543108	0.86[CHB][hapmap]
rs6543210	0.86[CHB][hapmap]
rs6709571	0.80[CHB][hapmap]
rs6710088	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6710813	0.86[CHB][hapmap]
rs6711101	1.00[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6738389	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6746768	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6748124	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6748809	0.80[CHB][hapmap]
rs6757357	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71412824	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71429376	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs717417	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7421146	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7564773	0.84[EUR][1000 genomes]
rs7567397	0.86[CHB][hapmap]
rs7583868	0.84[EUR][1000 genomes]
rs7601898	0.85[EUR][1000 genomes]
rs895438	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs953320	1.00[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98406400-98469200	Weak transcription	A549	lung
2	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
3	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
4	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:98428000-98466600	Weak transcription	K562	blood
6	chr2:98428600-98464600	Weak transcription	HSMMtube	muscle
7	chr2:98428800-98485000	Weak transcription	NHLF	lung
8	chr2:98429000-98470600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:98430000-98467800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:98431000-98466400	Weak transcription	NH-A	brain
11	chr2:98434200-98484000	Weak transcription	NHDF-Ad	bronchial
12	chr2:98434400-98466400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:98434400-98485800	Weak transcription	Lung	lung
14	chr2:98446000-98475000	Weak transcription	Gastric	stomach
15	chr2:98447400-98465400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:98447800-98466200	Weak transcription	Psoas Muscle	Psoas
17	chr2:98447800-98479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:98449600-98482000	Weak transcription	Fetal Kidney	kidney
20	chr2:98451800-98466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:98457000-98466400	Weak transcription	Osteobl	bone
22	chr2:98457000-98477400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:98457000-98477400	Weak transcription	Esophagus	oesophagus
24	chr2:98457000-98478000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:98457000-98485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:98457200-98466200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:98457200-98467600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:98457200-98485800	Weak transcription	Brain Anterior Caudate	brain
29	chr2:98457400-98466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:98457400-98485800	Weak transcription	Aorta	Aorta
31	chr2:98457600-98465800	Weak transcription	Brain Angular Gyrus	brain
32	chr2:98457600-98468200	Weak transcription	Fetal Thymus	thymus
33	chr2:98457600-98469000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:98457600-98475000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:98457600-98475000	Weak transcription	Fetal Stomach	stomach
36	chr2:98457600-98475000	Weak transcription	Pancreas	Pancrea
37	chr2:98457600-98475000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:98457600-98475000	Weak transcription	Spleen	Spleen
39	chr2:98457600-98475200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:98457600-98477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:98457600-98485400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:98457800-98466400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:98457800-98467600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:98457800-98467600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:98457800-98467800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:98457800-98473600	Weak transcription	Left Ventricle	heart
47	chr2:98457800-98474800	Weak transcription	Adipose Nuclei	Adipose
48	chr2:98457800-98475000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:98457800-98475200	Weak transcription	Thymus	Thymus
50	chr2:98457800-98478000	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links