Variant report

Variant	rs10897521
Chromosome Location	chr11:64391910-64391911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10128590	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792445	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10897519	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231837	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231838	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231841	0.81[AFR][1000 genomes]
rs11231842	0.90[YRI][hapmap]
rs11231848	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605121	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11820322	0.90[YRI][hapmap]
rs1207179	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1207226	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1212146	0.94[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12269736	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17146104	0.81[AFR][1000 genomes]
rs17146216	0.92[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2022051	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269730	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285339	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361216	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959654	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741399	0.92[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs3802947	0.92[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs471618	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490192	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs502567	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506035	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516117	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530252	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530775	0.93[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs557709	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55908793	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56105921	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57387921	0.83[AFR][1000 genomes]
rs61884406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7117423	0.94[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121121	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128467	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72927012	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7929296	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929627	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7932775	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937990	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948689	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10897521	NRXN2	cis	multi-tissue	Pritchard
rs10897521	NRXN2	cis	lung	GTEx

Chromatin state (count:61 , 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	chr11:64389200-64392800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:64389200-64395000	Weak transcription	Colonic Mucosa	Colon
17	chr11:64389200-64396200	Weak transcription	Brain Substantia Nigra	brain
18	chr11:64389200-64405200	Weak transcription	Fetal Kidney	kidney
19	chr11:64389400-64393000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:64389400-64394400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:64389400-64395000	Weak transcription	Fetal Lung	lung
22	chr11:64389400-64395800	Weak transcription	Ovary	ovary
23	chr11:64389400-64396400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr11:64389400-64396600	Strong transcription	Fetal Stomach	stomach
25	chr11:64389600-64392800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:64389600-64404800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:64389800-64397200	Weak transcription	Fetal Intestine Large	intestine
28	chr11:64389800-64397200	Weak transcription	Pancreas	Pancrea
29	chr11:64390000-64393200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:64390200-64392200	Weak transcription	HSMM	muscle
31	chr11:64390200-64394000	Strong transcription	Brain Hippocampus Middle	brain
32	chr11:64390200-64394600	Weak transcription	Thymus	Thymus
33	chr11:64390200-64395200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:64390200-64396800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:64390200-64399800	Strong transcription	Fetal Brain Female	brain
36	chr11:64390200-64405000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:64390400-64392400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:64390400-64393400	Genic enhancers	Fetal Muscle Leg	muscle
39	chr11:64390400-64394400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr11:64390400-64395000	Weak transcription	Brain Angular Gyrus	brain
41	chr11:64390400-64397000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:64390400-64398000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:64390600-64392400	Weak transcription	Fetal Intestine Small	intestine
44	chr11:64390600-64396000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:64390800-64392000	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr11:64390800-64392600	Weak transcription	Aorta	Aorta
47	chr11:64390800-64392600	Weak transcription	Spleen	Spleen
48	chr11:64391000-64394200	Strong transcription	Osteobl	bone
49	chr11:64391000-64394800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:64391000-64399400	Weak transcription	Fetal Brain Male	brain

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