Variant report

Variant	rs6592500
Chromosome Location	chr11:72651705-72651706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATG16L2-9	chr11:72651543-72652157	NONHSAT022807

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10793048	0.85[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10793049	0.92[YRI][hapmap]
rs10793055	0.86[YRI][hapmap]
rs10793056	0.86[YRI][hapmap]
rs10898881	0.95[YRI][hapmap]
rs10898885	0.92[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10898894	0.86[YRI][hapmap]
rs11235612	0.86[YRI][hapmap]
rs11822039	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12294037	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12294533	0.86[YRI][hapmap]
rs12805658	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12808517	0.84[CEU][hapmap]
rs2187494	0.92[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2276379	0.86[YRI][hapmap]
rs2303969	0.81[YRI][hapmap]
rs3862794	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3862796	0.92[CEU][hapmap]
rs4394861	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4944016	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs4944823	0.84[AFR][1000 genomes]
rs593753	0.92[CEU][hapmap]
rs6592505	0.84[CEU][hapmap]
rs6592508	0.86[YRI][hapmap]
rs6592509	0.84[CEU][hapmap]
rs6592510	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7108955	0.91[CEU][hapmap]
rs7126070	0.86[ASN][1000 genomes]
rs7925928	0.82[YRI][hapmap]
rs7936751	0.82[YRI][hapmap]
rs7937701	0.81[YRI][hapmap]
rs7943424	0.95[YRI][hapmap]
rs7946861	0.84[CEU][hapmap]
rs9645708	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3394774	chr11:72320884-72694077	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2422418	chr11:72646518-72807865	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv555411	chr11:72647296-72800970	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv983042	chr11:72651506-72652006	Enhancers Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72600800-72653200	Weak transcription	Lung	lung
2	chr11:72624200-72654400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:72624400-72652000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:72630800-72662400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:72633000-72654400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:72633000-72680000	Weak transcription	Dnd41	blood
7	chr11:72633000-72684000	Weak transcription	Primary T cells from cord blood	blood
8	chr11:72633200-72668400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:72633400-72679400	Weak transcription	Fetal Thymus	thymus
10	chr11:72636200-72694800	Weak transcription	Adipose Nuclei	Adipose
11	chr11:72636400-72680200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr11:72636400-72712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr11:72637000-72721600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:72637200-72653200	Weak transcription	Psoas Muscle	Psoas
15	chr11:72637400-72666000	Weak transcription	Ovary	ovary
16	chr11:72637400-72666400	Weak transcription	Right Ventricle	heart
17	chr11:72640400-72652400	Strong transcription	GM12878-XiMat	blood
18	chr11:72641200-72654400	Weak transcription	Fetal Kidney	kidney
19	chr11:72641800-72653200	Weak transcription	Pancreas	Pancrea
20	chr11:72641800-72680200	Weak transcription	HSMMtube	muscle
21	chr11:72643600-72676400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:72643800-72653000	Weak transcription	HSMM	muscle
23	chr11:72643800-72668400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:72643800-72673000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:72644000-72662000	Weak transcription	Osteobl	bone
26	chr11:72644600-72662000	Weak transcription	Liver	Liver
27	chr11:72645400-72652000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr11:72647200-72657000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:72647200-72670800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:72647200-72680800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:72647400-72662200	Weak transcription	Fetal Lung	lung
32	chr11:72648200-72651800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:72648400-72654000	Strong transcription	Primary B cells from cord blood	blood
34	chr11:72648800-72660200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:72648800-72661800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr11:72649000-72721600	Weak transcription	Thymus	Thymus
37	chr11:72649400-72652000	Enhancers	Fetal Heart	heart
38	chr11:72649600-72681600	Weak transcription	Aorta	Aorta
39	chr11:72649800-72652400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:72649800-72657800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:72649800-72679400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:72650400-72658000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:72650400-72666600	Weak transcription	HepG2	liver
44	chr11:72650800-72652000	Enhancers	Brain Angular Gyrus	brain
45	chr11:72650800-72654400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr11:72651000-72651800	Enhancers	Stomach Mucosa	stomach
47	chr11:72651000-72652000	Enhancers	Brain Substantia Nigra	brain
48	chr11:72651000-72653200	Weak transcription	Spleen	Spleen
49	chr11:72651400-72662400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:72651400-72666400	Weak transcription	HUVEC	blood vessel

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