Variant report

Variant	rs519090
Chromosome Location	chr11:64456240-64456241
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64455594..64456362-chr11:64510206..64510802,2	MCF-7	breast:
2	chr11:64455433..64456290-chr11:64492003..64492618,2	MCF-7	breast:
3	chr11:64426863..64427525-chr11:64455907..64456498,2	K562	blood:
4	chr11:64455658..64456677-chr11:64490650..64491647,6	K562	blood:
5	chr11:64256984..64257844-chr11:64455887..64456438,2	MCF-7	breast:
6	chr11:64455466..64456445-chr11:64535292..64535834,2	MCF-7	breast:
7	chr11:64455550..64457033-chr11:64471436..64472450,6	MCF-7	breast:
8	chr11:64455529..64456677-chr11:64490547..64491599,8	MCF-7	breast:
9	chr11:64454763..64457132-chr11:64459116..64461496,2	K562	blood:
10	chr11:64454637..64457192-chr11:64487658..64491640,3	K562	blood:
11	chr11:64420269..64421221-chr11:64455783..64456511,2	MCF-7	breast:
12	chr11:64456116..64458065-chr11:64530608..64532539,2	K562	blood:
13	chr11:64455051..64459063-chr11:64526543..64532108,4	K562	blood:
14	chr11:64455640..64456327-chr11:64471706..64472235,2	MCF-7	breast:
15	chr11:64455547..64456495-chr11:64490376..64491431,6	MCF-7	breast:
16	chr11:64455760..64456313-chr11:64531872..64532506,2	MCF-7	breast:
17	chr11:64455208..64457663-chr11:64463168..64465693,2	K562	blood:
18	chr11:64455279..64456563-chr11:64509970..64511034,11	MCF-7	breast:
19	chr11:64454221..64456529-chr11:64460067..64463247,3	MCF-7	breast:
20	chr11:64455524..64456500-chr11:64510043..64511654,4	K562	blood:
21	chr11:64419216..64421047-chr11:64455439..64457519,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168066	Chromatin interaction
ENSG00000068976	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000110076	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10792441	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10792443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10897518	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11231825	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11231845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11602903	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11606370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11607663	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12365089	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12786214	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12802649	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1529909	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2021860	0.83[AMR][1000 genomes];0.86[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];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2360872	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2360873	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]
rs2666559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666563	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35195142	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825016	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3825018	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs475642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs477138	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs492175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs495130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500531	0.90[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs504915	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs505802	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs506338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518053	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524023	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs526338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs528211	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs531763	0.82[ASN][1000 genomes]
rs537246	0.86[ASN][1000 genomes]
rs538737	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs544838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549461	0.85[ASN][1000 genomes]
rs552307	0.85[ASN][1000 genomes]
rs555456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs559946	0.87[ASN][1000 genomes]
rs561193	0.86[ASN][1000 genomes]
rs7102344	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7932437	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs80841	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893006	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs893007	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9734313	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs519090	NRXN2	cis	lung	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64453800-64456600	Enhancers	Fetal Brain Male	brain
2	chr11:64454400-64456600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:64454400-64456600	Enhancers	Liver	Liver
4	chr11:64455000-64456600	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr11:64455000-64456600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr11:64455400-64456400	Enhancers	Stomach Mucosa	stomach
7	chr11:64455600-64456400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr11:64455600-64456600	Flanking Active TSS	Fetal Muscle Trunk	muscle
9	chr11:64455800-64456400	Flanking Active TSS	Rectal Smooth Muscle	rectum
10	chr11:64455800-64456600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:64455800-64456600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:64455800-64456600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:64455800-64456600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:64455800-64456600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:64455800-64456600	Flanking Active TSS	Hela-S3	cervix
16	chr11:64455800-64456600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr11:64455800-64456800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr11:64456000-64456400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr11:64456000-64456400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr11:64456000-64456400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:64456000-64456400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:64456000-64456400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:64456000-64456400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:64456000-64456400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:64456000-64456400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:64456000-64456400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:64456000-64456400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr11:64456000-64456400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr11:64456000-64456400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr11:64456000-64456400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr11:64456000-64456400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:64456000-64456400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:64456000-64456400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:64456000-64456400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:64456000-64456400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr11:64456000-64456400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr11:64456000-64456400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr11:64456000-64456400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr11:64456000-64456400	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr11:64456000-64456400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr11:64456000-64456400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr11:64456000-64456400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr11:64456000-64456400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr11:64456000-64456400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr11:64456000-64456400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:64456000-64456400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr11:64456000-64456400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr11:64456000-64456400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:64456000-64456400	Active TSS	Muscle Satellite Cultured Cells	--
50	chr11:64456000-64456400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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