Variant report

Variant	rs12273892
Chromosome Location	chr11:64480930-64480931
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr11:64480587-64481250	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr11:64480666-64481103	A549	lung:	n/a	n/a
3	MAX	chr11:64480771-64480984	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr11:64480666-64481074	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr11:64480912-64481475	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr11:64480724-64481581	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr11:64480682-64481112	ECC-1	luminal epithelium:	n/a	n/a
8	E2F6	chr11:64480631-64481123	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr11:64480747-64480983	PANC-1	pancreas:	n/a	n/a
10	MAX	chr11:64480593-64481175	A549	lung:	n/a	n/a
11	MAX	chr11:64480611-64481190	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr11:64480534-64481152	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr11:64480448-64481115	H1-hESC	embryonic stem cell:	n/a	chr11:64480454-64480466
14	E2F6	chr11:64480777-64481089	K562	blood:	n/a	n/a
15	MAX	chr11:64480816-64481008	A549	lung:	n/a	n/a
16	BACH1	chr11:64479115-64481072	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr11:64480730-64481109	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64478005..64481824-chr11:64534394..64538447,4	K562	blood:
2	chr11:64478255..64481463-chr11:64489766..64492365,3	K562	blood:
3	chr11:64480253..64481992-chr11:64507131..64509338,2	K562	blood:

No data

Variant related genes	Relation type
NRXN2	TF binding region
ENSG00000168066	Chromatin interaction
ENSG00000110076	Chromatin interaction
ENSG00000068831	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11602411	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2666558	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666560	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825074	0.84[ASN][1000 genomes]
rs478607	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521793	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551890	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59739006	0.84[ASN][1000 genomes]
rs60159753	0.89[AMR][1000 genomes];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	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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
22	esv3436229	chr11:64478776-64483074	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	esv3405891	chr11:64479801-64482349	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	esv3433769	chr11:64480376-64482224	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12273892	NRXN2	cis	lung	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64477800-64481600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:64478000-64481000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:64478200-64481000	Enhancers	Gastric	stomach
4	chr11:64478600-64481600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr11:64478800-64481600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr11:64478800-64481600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:64479000-64481000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:64479400-64481000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:64479400-64481000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:64479600-64481800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr11:64479800-64481000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
12	chr11:64479800-64481000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
13	chr11:64479800-64481000	Enhancers	Fetal Heart	heart
14	chr11:64479800-64481400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr11:64479800-64481600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:64479800-64481600	Weak transcription	Brain Substantia Nigra	brain
17	chr11:64480000-64481600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr11:64480000-64481800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr11:64480200-64481000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:64480200-64481200	Enhancers	Primary hematopoietic stem cells	blood
21	chr11:64480200-64481400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr11:64480200-64481400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr11:64480200-64481400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
24	chr11:64480200-64481600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr11:64480200-64481600	Enhancers	Primary B cells from cord blood	blood
26	chr11:64480200-64481600	Bivalent Enhancer	Lung	lung
27	chr11:64480400-64481000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:64480400-64481000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:64480400-64481000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:64480400-64481200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
31	chr11:64480400-64481400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr11:64480400-64481400	Enhancers	Pancreas	Pancrea
33	chr11:64480400-64481400	Flanking Bivalent TSS/Enh	Thymus	Thymus
34	chr11:64480400-64481600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:64480400-64481800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr11:64480400-64489800	Enhancers	Fetal Brain Male	brain
37	chr11:64480600-64481000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:64480600-64481000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:64480600-64481000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:64480600-64481000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:64480600-64481000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:64480600-64481000	Flanking Bivalent TSS/Enh	Spleen	Spleen
43	chr11:64480600-64481200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:64480600-64481200	Bivalent/Poised TSS	Psoas Muscle	Psoas
45	chr11:64480600-64481200	Bivalent Enhancer	Small Intestine	intestine
46	chr11:64480600-64481600	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr11:64480600-64481600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
48	chr11:64480800-64481000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:64480800-64481000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:64480800-64481000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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