Variant report

Variant	rs478607
Chromosome Location	chr11:64478063-64478064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64478005..64481824-chr11:64534394..64538447,4	K562	blood:
2	chr11:64476395..64479259-chr11:64497435..64499658,2	K562	blood:
3	chr11:64472309..64475005-chr11:64477653..64479345,2	MCF-7	breast:
4	chr11:64471601..64473400-chr11:64476354..64479027,3	MCF-7	breast:
5	chr11:64477247..64478814-chr11:64479470..64481853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168066	Chromatin interaction
ENSG00000110076	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11602411	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12273892	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666558	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666560	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825074	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs521793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551890	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59739006	0.84[ASN][1000 genomes]
rs60159753	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884374	0.84[ASN][1000 genomes]
rs61884411	0.86[ASN][1000 genomes]
rs61884413	0.83[EUR][1000 genomes]
rs61884449	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	79 gene(s)	inside rSNPs	diseases
14	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
17	nsv359	chr11:64477008-64502873	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
18	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
19	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer 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
21	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS 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

Variant related diseases (count:1)

Disease	PMID	Source
Urate levels	23263486	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs478607	NRXN2	cis	lung	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64473400-64478400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:64477000-64478400	Enhancers	Fetal Brain Male	brain
3	chr11:64477600-64478200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr11:64477600-64478600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr11:64477600-64478800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:64477800-64478200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr11:64477800-64478200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:64477800-64478400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr11:64477800-64478400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:64477800-64478400	Enhancers	HSMM	muscle
11	chr11:64477800-64478600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:64477800-64478600	Enhancers	H9 Cell Line	embryonic stem cell
13	chr11:64477800-64478600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr11:64477800-64478600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr11:64477800-64478600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:64477800-64478600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
17	chr11:64477800-64478600	Enhancers	Brain Angular Gyrus	brain
18	chr11:64477800-64478600	Enhancers	A549	lung
19	chr11:64477800-64478600	Bivalent Enhancer	Osteobl	bone
20	chr11:64477800-64478800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:64477800-64478800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:64477800-64478800	Enhancers	Hela-S3	cervix
23	chr11:64477800-64479400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr11:64477800-64479600	Enhancers	K562	blood
25	chr11:64477800-64479800	Enhancers	Brain Substantia Nigra	brain
26	chr11:64477800-64479800	Flanking Active TSS	Fetal Brain Female	brain
27	chr11:64477800-64481600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:64478000-64478200	Bivalent Enhancer	GM12878-XiMat	blood
29	chr11:64478000-64478200	Enhancers	HSMMtube	muscle
30	chr11:64478000-64478400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
31	chr11:64478000-64478400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
32	chr11:64478000-64478400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
33	chr11:64478000-64478600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:64478000-64478600	Enhancers	Brain Cingulate Gyrus	brain
35	chr11:64478000-64478600	Bivalent Enhancer	Stomach Mucosa	stomach
36	chr11:64478000-64478800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:64478000-64478800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:64478000-64478800	Bivalent Enhancer	NH-A	brain
39	chr11:64478000-64479000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
40	chr11:64478000-64479200	Enhancers	Brain Hippocampus Middle	brain
41	chr11:64478000-64479200	Bivalent Enhancer	Fetal Kidney	kidney
42	chr11:64478000-64479200	Bivalent Enhancer	Fetal Lung	lung
43	chr11:64478000-64479400	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr11:64478000-64480000	Enhancers	Brain Anterior Caudate	brain
45	chr11:64478000-64480200	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr11:64478000-64480800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:64478000-64480800	Weak transcription	Right Atrium	heart
48	chr11:64478000-64481000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links