Variant report

Variant	rs2360873
Chromosome Location	chr11:64391157-64391158
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10792441	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10792443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897518	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231825	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11602903	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607663	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362590	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12365089	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12786214	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12802649	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1529909	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2021860	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2360872	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2666559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2666563	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35195142	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825016	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825018	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs475642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs477138	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs492175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4930556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs500531	0.90[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs504915	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs505802	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs506338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518053	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs519090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs524023	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs528211	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531763	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs537246	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs538737	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs544838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs549461	0.85[ASN][1000 genomes]
rs552307	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs555456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs559946	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs561193	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7102344	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932437	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs80841	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs893006	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs893007	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9734313	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
9	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
10	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
11	nsv897696	chr11:64365796-64412877	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
14	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	esv3444725	chr11:64391096-64391386	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2360873	NRXN2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64373600-64402200	Weak transcription	HSMMtube	muscle
2	chr11:64380000-64396800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:64380800-64396600	Weak transcription	NHDF-Ad	bronchial
4	chr11:64387400-64394600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:64387400-64394800	Enhancers	Primary hematopoietic stem cells	blood
6	chr11:64388000-64404600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr11:64388600-64397200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:64388600-64405400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:64388800-64392600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:64388800-64393600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:64388800-64393600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:64388800-64405400	Weak transcription	Right Atrium	heart
13	chr11:64389000-64394600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:64389000-64397400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:64389200-64391200	Genic enhancers	Brain Germinal Matrix	brain
16	chr11:64389200-64391800	Weak transcription	Brain Anterior Caudate	brain
17	chr11:64389200-64392800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:64389200-64395000	Weak transcription	Colonic Mucosa	Colon
19	chr11:64389200-64396200	Weak transcription	Brain Substantia Nigra	brain
20	chr11:64389200-64405200	Weak transcription	Fetal Kidney	kidney
21	chr11:64389400-64391600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:64389400-64391600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:64389400-64391800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:64389400-64393000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:64389400-64394400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:64389400-64395000	Weak transcription	Fetal Lung	lung
27	chr11:64389400-64395800	Weak transcription	Ovary	ovary
28	chr11:64389400-64396400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr11:64389400-64396600	Strong transcription	Fetal Stomach	stomach
30	chr11:64389600-64391800	Weak transcription	Primary B cells from cord blood	blood
31	chr11:64389600-64392800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:64389600-64404800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:64389800-64397200	Weak transcription	Fetal Intestine Large	intestine
34	chr11:64389800-64397200	Weak transcription	Pancreas	Pancrea
35	chr11:64390000-64391600	Strong transcription	Colon Smooth Muscle	Colon
36	chr11:64390000-64393200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:64390200-64391400	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr11:64390200-64392200	Weak transcription	HSMM	muscle
39	chr11:64390200-64394000	Strong transcription	Brain Hippocampus Middle	brain
40	chr11:64390200-64394600	Weak transcription	Thymus	Thymus
41	chr11:64390200-64395200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr11:64390200-64396800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:64390200-64399800	Strong transcription	Fetal Brain Female	brain
44	chr11:64390200-64405000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:64390400-64392400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:64390400-64393400	Genic enhancers	Fetal Muscle Leg	muscle
47	chr11:64390400-64394400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr11:64390400-64395000	Weak transcription	Brain Angular Gyrus	brain
49	chr11:64390400-64397000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:64390400-64398000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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