Variant report

Variant	rs228593
Chromosome Location	chr11:108141134-108141135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10890813	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10890819	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap]
rs10890825	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11212515	0.94[CEU][hapmap]
rs1150201	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12226046	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs170548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs179110	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs227060	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs228606	0.81[GIH][hapmap]
rs373759	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs3741056	0.89[CEU][hapmap]
rs4615991	0.87[CEU][hapmap]
rs4987982	0.81[JPT][hapmap]
rs592955	0.81[JPT][hapmap]
rs597788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs609261	0.81[JPT][hapmap]
rs618499	0.81[JPT][hapmap]
rs61913701	0.83[EUR][1000 genomes]
rs619972	0.90[JPT][hapmap]
rs624366	0.81[JPT][hapmap]
rs645485	0.81[JPT][hapmap]
rs651030	0.83[ASN][1000 genomes]
rs654005	0.81[JPT][hapmap]
rs664677	0.81[JPT][hapmap]
rs665293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114794	1.00[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap]
rs920679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898383	chr11:108068954-108251211	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv556430	chr11:108097333-108175462	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv898384	chr11:108097333-108251211	Weak transcription Genic enhancers ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv898385	chr11:108123189-108165736	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv832262	chr11:108123831-108309350	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs228593	ACAT1	cis	cerebellum	SCAN
rs228593	NPAT	cis	cerebellum	SCAN
rs228593	ACAT1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108094800-108147400	Weak transcription	Esophagus	oesophagus
2	chr11:108094800-108244400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:108096000-108148600	Weak transcription	Fetal Heart	heart
4	chr11:108096400-108156400	Weak transcription	NHLF	lung
5	chr11:108104200-108147400	Weak transcription	Gastric	stomach
6	chr11:108104600-108144000	Weak transcription	Lung	lung
7	chr11:108108200-108144200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:108108400-108184800	Weak transcription	NHEK	skin
9	chr11:108108800-108147600	Weak transcription	Psoas Muscle	Psoas
10	chr11:108113800-108147200	Weak transcription	Aorta	Aorta
11	chr11:108122000-108142200	Weak transcription	Right Ventricle	heart
12	chr11:108122000-108147400	Weak transcription	Spleen	Spleen
13	chr11:108126000-108142000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:108126000-108153600	Weak transcription	HUVEC	blood vessel
15	chr11:108126200-108157600	Weak transcription	HMEC	breast
16	chr11:108126800-108149200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:108128800-108142600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:108129000-108143200	Weak transcription	Ovary	ovary
19	chr11:108129000-108145800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:108129000-108148000	Weak transcription	Pancreas	Pancrea
21	chr11:108129000-108155400	Weak transcription	HSMMtube	muscle
22	chr11:108129200-108142000	Weak transcription	Fetal Kidney	kidney
23	chr11:108129400-108142200	Weak transcription	Brain Angular Gyrus	brain
24	chr11:108129600-108142000	Weak transcription	Brain Anterior Caudate	brain
25	chr11:108129600-108142000	Weak transcription	Fetal Brain Male	brain
26	chr11:108129800-108141800	Weak transcription	K562	blood
27	chr11:108129800-108142000	Weak transcription	Brain Substantia Nigra	brain
28	chr11:108129800-108146600	Weak transcription	Colonic Mucosa	Colon
29	chr11:108129800-108147400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr11:108130600-108143000	Weak transcription	NH-A	brain
31	chr11:108131200-108141800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr11:108131200-108145400	Weak transcription	Fetal Intestine Large	intestine
33	chr11:108131200-108147400	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:108131400-108141400	Weak transcription	Brain Germinal Matrix	brain
35	chr11:108131400-108142000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:108131400-108142200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:108131400-108142200	Weak transcription	A549	lung
38	chr11:108131400-108147400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:108131600-108142000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:108131600-108142000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:108131600-108142200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr11:108131600-108142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:108131600-108143000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:108131800-108142600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:108131800-108144200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:108131800-108144200	Weak transcription	Left Ventricle	heart
47	chr11:108131800-108147200	Weak transcription	Thymus	Thymus
48	chr11:108131800-108147400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:108131800-108209600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr11:108132200-108142000	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links