Variant report

Variant	rs2276379
Chromosome Location	chr11:72758353-72758354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10437750	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793048	0.86[YRI][hapmap]
rs10793049	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs10793054	0.95[YRI][hapmap]
rs10793055	0.85[ASW][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10793056	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10898885	0.86[YRI][hapmap]
rs10898894	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898895	0.87[CHB][hapmap];0.95[YRI][hapmap]
rs10898896	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10898900	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11235612	0.86[CHB][hapmap];0.82[CHD][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs11235651	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12288580	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12289752	0.81[ASN][1000 genomes]
rs12293726	0.81[ASN][1000 genomes]
rs12294533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1982585	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2187494	0.82[YRI][hapmap]
rs4394861	0.86[YRI][hapmap]
rs55671951	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6592500	0.86[YRI][hapmap]
rs6592508	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7104158	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7925928	0.95[YRI][hapmap]
rs7936751	0.95[YRI][hapmap]
rs7937701	0.96[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7943424	0.80[ASW][hapmap];0.89[GIH][hapmap];0.91[YRI][hapmap]
rs9645708	0.91[CHB][hapmap];0.82[CHD][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][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	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
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2276379	KRTAP5-11	cis	cerebellum	SCAN
rs2276379	ATG16L2	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72724400-72761000	Weak transcription	HSMM	muscle
2	chr11:72739200-72759200	Weak transcription	Aorta	Aorta
3	chr11:72739400-72765800	Weak transcription	Spleen	Spleen
4	chr11:72739600-72759200	Weak transcription	Osteobl	bone
5	chr11:72740000-72758400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:72740000-72758800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:72740000-72759200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:72740000-72771800	Weak transcription	Fetal Stomach	stomach
9	chr11:72740800-72758400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr11:72741400-72765000	Weak transcription	Fetal Heart	heart
11	chr11:72743800-72758800	Weak transcription	HUVEC	blood vessel
12	chr11:72744200-72759200	Weak transcription	Pancreas	Pancrea
13	chr11:72744600-72758600	Weak transcription	Fetal Intestine Small	intestine
14	chr11:72745600-72761000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:72746200-72759200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:72746400-72759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:72746600-72758400	Weak transcription	Primary T cells from cord blood	blood
18	chr11:72746600-72758400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:72746600-72758600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:72746600-72759200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr11:72746600-72759400	Weak transcription	Left Ventricle	heart
22	chr11:72746600-72824600	Weak transcription	Thymus	Thymus
23	chr11:72746800-72759200	Weak transcription	Fetal Thymus	thymus
24	chr11:72747400-72758400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:72747400-72758600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:72747600-72759200	Weak transcription	Dnd41	blood
27	chr11:72747800-72758800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:72749000-72758400	Weak transcription	Brain Anterior Caudate	brain
29	chr11:72750400-72758600	Weak transcription	HepG2	liver
30	chr11:72750600-72758400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:72750600-72759200	Weak transcription	Fetal Intestine Large	intestine
32	chr11:72750600-72765800	Weak transcription	Ovary	ovary
33	chr11:72750800-72759000	Weak transcription	Placenta	Placenta
34	chr11:72751400-72759200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:72753000-72758400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:72753600-72758600	Weak transcription	Fetal Lung	lung
37	chr11:72755000-72758400	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:72755400-72758800	Weak transcription	Brain Angular Gyrus	brain
39	chr11:72756800-72759200	Enhancers	Primary B cells from peripheral blood	blood
40	chr11:72757000-72758400	Enhancers	Primary B cells from cord blood	blood
41	chr11:72757200-72758400	Enhancers	GM12878-XiMat	blood
42	chr11:72757600-72759000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr11:72757800-72758400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr11:72757800-72758400	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr11:72757800-72758600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:72757800-72758800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr11:72757800-72759800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr11:72758000-72758400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr11:72758000-72758800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr11:72758200-72759400	Enhancers	Pancreatic Islets	Pancreatic Islet

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