Variant report

Variant	rs11024256
Chromosome Location	chr11:17354775-17354776
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NUCB2-3	chr11:17353589-17356027	NONHSAT018224

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10219196	0.98[ASN][1000 genomes]
rs10430892	0.86[CHB][hapmap]
rs10466382	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs10766383	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs10766384	0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs10766385	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.97[ASN][1000 genomes]
rs10766387	0.98[ASN][1000 genomes]
rs10766389	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs10766390	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap]
rs10766391	0.91[CHB][hapmap]
rs10832756	0.81[CHB][hapmap]
rs10832757	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs10832758	0.95[ASN][1000 genomes]
rs10832759	0.97[ASN][1000 genomes]
rs10832760	0.97[ASN][1000 genomes]
rs10832762	0.98[ASN][1000 genomes]
rs10832763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832764	0.98[ASN][1000 genomes]
rs10832765	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.98[ASN][1000 genomes]
rs10832768	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.98[ASN][1000 genomes]
rs10832769	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.97[ASN][1000 genomes]
rs10832770	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10832771	0.85[ASN][1000 genomes]
rs10832772	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10832773	0.83[ASN][1000 genomes]
rs10832774	0.86[ASN][1000 genomes]
rs10832775	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10832779	0.91[CHB][hapmap]
rs10832781	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap]
rs10832782	0.86[CHB][hapmap]
rs11024243	0.83[CHB][hapmap]
rs11024246	0.95[CHB][hapmap]
rs11024250	0.97[ASN][1000 genomes]
rs11024251	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11024253	0.98[ASN][1000 genomes]
rs11024254	0.98[ASN][1000 genomes]
rs11024260	0.98[ASN][1000 genomes]
rs11024262	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11024263	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11024272	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs11525338	0.98[ASN][1000 genomes]
rs12225041	0.97[ASN][1000 genomes]
rs12282915	0.82[CHB][hapmap]
rs2018218	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2354867	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4582955	0.98[ASN][1000 genomes]
rs4756887	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs67904954	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799280	chr11:17299390-17354775	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	esv1801731	chr11:17299390-17354775	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11024256	ABCC8	cis	cerebellum	SCAN
rs11024256	LOC494141	cis	lymphoblastoid	seeQTL
rs11024256	ABCC8	cis	parietal	SCAN
rs11024256	PLEKHA7	cis	parietal	SCAN
rs11024256	SERGEF	cis	parietal	SCAN
rs11024256	KCNJ11	cis	cerebellum	SCAN
rs11024256	GTF2H1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17299000-17357200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:17299000-17357600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:17299000-17360600	Weak transcription	Small Intestine	intestine
4	chr11:17299200-17357000	Weak transcription	Brain Substantia Nigra	brain
5	chr11:17299400-17355400	Weak transcription	Brain Angular Gyrus	brain
6	chr11:17299400-17357000	Weak transcription	Fetal Intestine Large	intestine
7	chr11:17308200-17357600	Weak transcription	HepG2	liver
8	chr11:17308200-17360800	Strong transcription	Fetal Thymus	thymus
9	chr11:17308200-17372600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:17308400-17356800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:17308400-17361600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:17309000-17355600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:17312200-17355400	Weak transcription	Fetal Kidney	kidney
14	chr11:17316000-17360000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:17316000-17361000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:17318400-17355600	Weak transcription	Gastric	stomach
17	chr11:17319000-17356400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr11:17320800-17372400	Weak transcription	GM12878-XiMat	blood
19	chr11:17322600-17356200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:17326400-17358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:17330200-17358000	Weak transcription	K562	blood
22	chr11:17331800-17357400	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:17331800-17362000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:17334000-17371000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:17335400-17355600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:17335400-17356000	Weak transcription	Colonic Mucosa	Colon
27	chr11:17335600-17361000	Strong transcription	Dnd41	blood
28	chr11:17335800-17357200	Weak transcription	Fetal Brain Male	brain
29	chr11:17335800-17357600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:17336000-17355000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:17336200-17355000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:17336200-17372600	Weak transcription	HUVEC	blood vessel
33	chr11:17336400-17355800	Weak transcription	Psoas Muscle	Psoas
34	chr11:17336400-17360800	Weak transcription	HSMM	muscle
35	chr11:17336600-17355000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr11:17336800-17358400	Weak transcription	Brain Germinal Matrix	brain
37	chr11:17336800-17365000	Weak transcription	NHEK	skin
38	chr11:17341800-17355400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:17346800-17356000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr11:17348200-17356200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr11:17348400-17357000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:17348600-17355000	Strong transcription	Primary T cells from cord blood	blood
43	chr11:17348600-17356200	Strong transcription	Placenta	Placenta
44	chr11:17348800-17356000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:17349800-17356200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:17350000-17355000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr11:17350000-17356200	Strong transcription	Osteobl	bone
48	chr11:17350200-17355400	Weak transcription	HSMMtube	muscle
49	chr11:17350200-17356400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr11:17350400-17365200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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