Variant report

Variant	rs2269730
Chromosome Location	chr11:64423831-64423832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:64423561-64424159	A549	lung:	n/a	chr11:64423877-64423888 chr11:64423859-64423870
2	MYC	chr11:64423816-64423921	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr11:64423666-64424037	MCF10A-Er-Src	breast:	n/a	n/a
4	RAD21	chr11:64423717-64424081	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr11:64421262-64425000	U87	brain:	n/a	n/a
6	POLR2A	chr11:64421300-64425022	U87	brain:	n/a	n/a
7	STAT3	chr11:64423718-64424053	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr11:64423767-64424146	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr11:64423720-64424136	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr11:64411167-64429413	U87	brain:	n/a	n/a
11	FOS	chr11:64423826-64424127	MCF10A-Er-Src	breast:	n/a	n/a
12	BRCA1	chr11:64423620-64424196	Hela-S3	cervix:	n/a	n/a
13	GTF2F1	chr11:64423732-64424244	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr11:64423694-64424067	HepG2	liver:	n/a	chr11:64423877-64423888 chr11:64423859-64423870
15	RFX5	chr11:64423718-64424223	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr11:64414444-64429407	U87	brain:	n/a	n/a
17	CEBPB	chr11:64423698-64424067	A549	lung:	n/a	chr11:64423877-64423888 chr11:64423859-64423870
18	MXI1	chr11:64423660-64424219	Hela-S3	cervix:	n/a	n/a
19	RCOR1	chr11:64423695-64424398	Hela-S3	cervix:	n/a	n/a
20	STAT3	chr11:64423739-64424021	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr11:64423718-64424008	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr11:64423778-64424044	Hela-S3	cervix:	n/a	n/a
23	TFAP2A	chr11:64423534-64424399	Hela-S3	cervix:	n/a	n/a
24	TBP	chr11:64423785-64424075	Hela-S3	cervix:	n/a	n/a
25	EP300	chr11:64423704-64424122	Hela-S3	cervix:	n/a	n/a
26	NFYB	chr11:64423730-64424113	Hela-S3	cervix:	n/a	n/a
27	SMC3	chr11:64423492-64424092	Hela-S3	cervix:	n/a	n/a
28	CHD2	chr11:64423800-64424129	Hela-S3	cervix:	n/a	n/a
29	MAX	chr11:64423477-64424225	Hela-S3	cervix:	n/a	n/a
30	MAZ	chr11:64423695-64424186	Hela-S3	cervix:	n/a	n/a
31	TCF7L2	chr11:64423575-64424138	Hela-S3	cervix:	n/a	n/a
32	CEBPB	chr11:64423682-64424070	IMR90	lung:	n/a	chr11:64423877-64423888 chr11:64423859-64423870
33	MYC	chr11:64423720-64424037	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr11:64423610-64424092	Hela-S3	cervix:	n/a	n/a
35	CEBPB	chr11:64423816-64423912	K562	blood:	n/a	chr11:64423877-64423888 chr11:64423859-64423870
36	CEBPB	chr11:64423469-64424229	Hela-S3	cervix:	n/a	chr11:64423877-64423888 chr11:64423859-64423870
37	TFAP2C	chr11:64423427-64424573	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64423611..64425758-chr11:64437675..64439983,2	K562	blood:
2	chr11:64418565..64420140-chr11:64423624..64426189,2	K562	blood:

Variant related genes	Relation type
NRXN2	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10128590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792445	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10897519	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897521	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]
rs11231837	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231838	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231842	0.90[YRI][hapmap]
rs11231848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231849	0.81[AFR][1000 genomes]
rs11605121	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11820322	0.90[YRI][hapmap]
rs1207179	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1207226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1212146	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12269736	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17146216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2022051	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957564	0.82[EUR][1000 genomes]
rs2959654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741399	1.00[YRI][hapmap]
rs3802947	1.00[YRI][hapmap]
rs471618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs502567	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516117	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs557709	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55908793	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56105921	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884406	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7117423	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72927012	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7929296	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929627	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7932775	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937990	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
12	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
13	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2269730	NRXN2	cis	lung	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64411600-64427800	Weak transcription	Aorta	Aorta
2	chr11:64412400-64428200	Weak transcription	Right Atrium	heart
3	chr11:64412600-64425600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:64415800-64430000	Weak transcription	Gastric	stomach
5	chr11:64420200-64426200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:64420400-64424000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr11:64420400-64424800	Enhancers	Adipose Nuclei	Adipose
8	chr11:64420400-64425000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:64420400-64425200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr11:64420400-64427800	Enhancers	Fetal Thymus	thymus
11	chr11:64420600-64424000	Enhancers	Primary B cells from cord blood	blood
12	chr11:64420600-64426600	Weak transcription	A549	lung
13	chr11:64420800-64426400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:64421000-64424000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:64421000-64424000	Weak transcription	Thymus	Thymus
16	chr11:64421000-64424800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:64421000-64425000	Weak transcription	Fetal Brain Female	brain
18	chr11:64421000-64425200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:64421000-64427200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:64421000-64434800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:64421200-64427000	Weak transcription	Brain Angular Gyrus	brain
22	chr11:64421200-64453800	Weak transcription	Fetal Brain Male	brain
23	chr11:64421400-64428600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:64421800-64424800	Enhancers	Placenta	Placenta
25	chr11:64422000-64425000	Enhancers	Liver	Liver
26	chr11:64422200-64424000	Enhancers	Spleen	Spleen
27	chr11:64422200-64424400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr11:64422200-64424600	Enhancers	Primary hematopoietic stem cells	blood
29	chr11:64422200-64424600	Enhancers	Brain Hippocampus Middle	brain
30	chr11:64422400-64424000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:64422400-64427200	Weak transcription	Brain Substantia Nigra	brain
32	chr11:64422600-64424800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:64422800-64427400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:64423000-64424400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:64423000-64424400	Enhancers	Osteobl	bone
36	chr11:64423000-64424600	Flanking Active TSS	Hela-S3	cervix
37	chr11:64423000-64430400	Strong transcription	Brain Germinal Matrix	brain
38	chr11:64423000-64432800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:64423200-64424000	Enhancers	Brain Anterior Caudate	brain
40	chr11:64423200-64424400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:64423200-64424400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:64423200-64424600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:64423400-64424400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:64423400-64424600	Enhancers	Fetal Muscle Leg	muscle
45	chr11:64423400-64425000	Enhancers	HSMMtube	muscle
46	chr11:64423400-64425200	Enhancers	HSMM	muscle
47	chr11:64423600-64424000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:64423600-64424200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr11:64423600-64424200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:64423600-64425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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