Variant report

Variant	rs2279900
Chromosome Location	chr11:18503159-18503160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18502477..18505271-chr11:18547847..18549412,2	K562	blood:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10219166	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10500835	0.86[TSI][hapmap]
rs10832938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832942	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10832943	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10832945	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024670	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024671	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024674	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024675	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024676	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024677	0.91[TSI][hapmap]
rs11024678	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024679	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024683	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024685	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024688	0.90[TSI][hapmap]
rs11024689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024695	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024696	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024706	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024716	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024723	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024724	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12049851	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12049909	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12049912	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12222154	0.86[TSI][hapmap]
rs12222210	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12223858	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12223887	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12225461	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12225463	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12289223	0.86[TSI][hapmap]
rs12290527	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12418726	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12419360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12419592	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12420702	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12420882	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12421881	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12574333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12575390	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12577874	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12803251	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16914838	0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16935504	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935575	0.86[TSI][hapmap]
rs2271080	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279902	0.91[TSI][hapmap]
rs2305166	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28607050	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3781639	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781640	0.91[TSI][hapmap]
rs4436523	0.81[TSI][hapmap]
rs4757673	0.95[JPT][hapmap]
rs55964013	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55999230	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56097703	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56151250	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56151849	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56411332	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59032896	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882885	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61882887	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61882903	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882904	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61884677	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7108487	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7109314	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7130163	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72871737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72876745	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7950602	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9633899	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2279900	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs2279900	UEVLD	cis	cerebellum	SCAN
rs2279900	LDHC	cis	parietal	SCAN
rs2279900	TSG101	cis	lymphoblastoid	seeQTL
rs2279900	NUCB2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18483600-18526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:18494400-18508000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:18494800-18507600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:18495000-18505800	Strong transcription	Thymus	Thymus
5	chr11:18496000-18508200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:18496000-18515200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr11:18496200-18503600	Weak transcription	Hela-S3	cervix
8	chr11:18496200-18508000	Strong transcription	Fetal Intestine Large	intestine
9	chr11:18496200-18508000	Strong transcription	Fetal Thymus	thymus
10	chr11:18496200-18508000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr11:18496200-18508200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:18496200-18513200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:18496200-18513400	Strong transcription	Fetal Muscle Leg	muscle
14	chr11:18496200-18538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:18496400-18506000	Strong transcription	Osteobl	bone
17	chr11:18496400-18506600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:18496400-18507800	Strong transcription	Dnd41	blood
19	chr11:18496400-18508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:18496400-18508200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr11:18496400-18508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:18496400-18508200	Strong transcription	Liver	Liver
23	chr11:18496400-18510000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:18496600-18506400	Strong transcription	Primary T cells from cord blood	blood
26	chr11:18496600-18507800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:18496600-18507800	Strong transcription	Adipose Nuclei	Adipose
28	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:18496800-18506000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:18496800-18506000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:18496800-18506400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:18496800-18506400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:18496800-18507800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:18496800-18509600	Strong transcription	HSMM	muscle
36	chr11:18497000-18505800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:18497000-18506200	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:18497000-18506200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:18497000-18511600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr11:18497000-18513200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:18497200-18513200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:18497400-18506200	Strong transcription	Brain Hippocampus Middle	brain
43	chr11:18497600-18504600	Strong transcription	Right Ventricle	heart
44	chr11:18497600-18506000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:18497600-18508200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:18497600-18513200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:18497800-18503800	Strong transcription	Psoas Muscle	Psoas
48	chr11:18497800-18504200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr11:18497800-18505800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:18497800-18506000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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