Variant report

Variant	rs2279902
Chromosome Location	chr11:18505632-18505633
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	chr11:18416882..18418570-chr11:18504246..18506790,2	K562	blood:

Variant related genes	Relation type
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10500835	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024669	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024693	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024706	0.85[TSI][hapmap]
rs11024714	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11024715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11024725	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11024726	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11024727	1.00[JPT][hapmap];0.85[TSI][hapmap]
rs12222154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12289223	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs12418726	0.85[TSI][hapmap]
rs12421394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12574333	0.91[TSI][hapmap]
rs16914838	0.81[TSI][hapmap]
rs16935541	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16935559	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16935575	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979051	0.94[JPT][hapmap]
rs1983124	0.95[JPT][hapmap]
rs2279900	0.91[TSI][hapmap]
rs2291751	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305166	0.85[TSI][hapmap]
rs3781640	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4436523	0.95[JPT][hapmap];0.90[TSI][hapmap]
rs55969503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882886	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61884673	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61884715	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61884716	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61884723	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61884724	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61886140	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61886141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6416020	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7950602	0.85[TSI][hapmap]

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
rs2279902	NUCB2	cis	cerebellum	SCAN
rs2279902	TSG101	cis	lymphoblastoid	seeQTL
rs2279902	LDHC	cis	parietal	SCAN
rs2279902	UEVLD	cis	cerebellum	SCAN
rs2279902	TSG101	Cis_1M	lymphoblastoid	RTeQTL

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	chr11:18496200-18508000	Strong transcription	Fetal Intestine Large	intestine
8	chr11:18496200-18508000	Strong transcription	Fetal Thymus	thymus
9	chr11:18496200-18508000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr11:18496200-18508200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:18496200-18513200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:18496200-18513400	Strong transcription	Fetal Muscle Leg	muscle
13	chr11:18496200-18538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:18496400-18506000	Strong transcription	Osteobl	bone
16	chr11:18496400-18506600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:18496400-18507800	Strong transcription	Dnd41	blood
18	chr11:18496400-18508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:18496400-18508200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:18496400-18508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:18496400-18508200	Strong transcription	Liver	Liver
22	chr11:18496400-18510000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr11:18496600-18506400	Strong transcription	Primary T cells from cord blood	blood
25	chr11:18496600-18507800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:18496600-18507800	Strong transcription	Adipose Nuclei	Adipose
27	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:18496800-18506000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:18496800-18506000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:18496800-18506400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:18496800-18506400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:18496800-18507800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:18496800-18509600	Strong transcription	HSMM	muscle
35	chr11:18497000-18505800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:18497000-18506200	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:18497000-18506200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr11:18497000-18511600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:18497000-18513200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:18497200-18513200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:18497400-18506200	Strong transcription	Brain Hippocampus Middle	brain
42	chr11:18497600-18506000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:18497600-18508200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:18497600-18513200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:18497800-18505800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:18497800-18506000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:18497800-18506200	Strong transcription	Lung	lung
48	chr11:18497800-18506200	Strong transcription	Ovary	ovary
49	chr11:18497800-18507400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:18497800-18512200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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