Variant report

Variant	rs11231848
Chromosome Location	chr11:64424369-64424370
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	CTCF	chr11:64424360-64424510	HA-sp	spinal cord:	n/a	chr11:64424441-64424448
2	POLR2A	chr11:64421262-64425000	U87	brain:	n/a	n/a
3	POLR2A	chr11:64421300-64425022	U87	brain:	n/a	n/a
4	CTCF	chr11:64424340-64424490	SK-N-SH_RA	brain:	n/a	chr11:64424441-64424448
5	CTCF	chr11:64424294-64424612	K562	blood:	n/a	chr11:64424529-64424542 chr11:64424441-64424448 chr11:64424321-64424334
6	UBTF	chr11:64424366-64424646	K562	blood:	n/a	n/a
7	GABPA	chr11:64424196-64424661	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr11:64424360-64424510	HCT-116	colon:	n/a	chr11:64424441-64424448
9	SMC3	chr11:64424351-64424558	K562	blood:	n/a	chr11:64424529-64424539
10	CTCF	chr11:64424340-64424490	Hela-S3	cervix:	n/a	chr11:64424441-64424448
11	POLR2A	chr11:64411167-64429413	U87	brain:	n/a	n/a
12	ZNF143	chr11:64424302-64424594	H1-hESC	embryonic stem cell:	n/a	n/a
13	JUND	chr11:64424331-64424564	K562	blood:	n/a	chr11:64424337-64424346
14	CTCF	chr11:64424339-64424550	K562	blood:	n/a	chr11:64424529-64424542 chr11:64424441-64424448
15	RAD21	chr11:64424229-64424574	H1-hESC	embryonic stem cell:	n/a	chr11:64424441-64424450 chr11:64424529-64424539 chr11:64424528-64424541 chr11:64424432-64424451 chr11:64424318-64424332 chr11:64424465-64424479
16	CTCF	chr11:64424340-64424490	HCPEpiC	choroid plexus:	n/a	chr11:64424441-64424448
17	RAD21	chr11:64424249-64424604	H1-hESC	embryonic stem cell:	n/a	chr11:64424441-64424450 chr11:64424529-64424539 chr11:64424528-64424541 chr11:64424432-64424451 chr11:64424318-64424332 chr11:64424465-64424479
18	RAD21	chr11:64424311-64424539	K562	blood:	n/a	chr11:64424441-64424450 chr11:64424529-64424539 chr11:64424432-64424451 chr11:64424318-64424332 chr11:64424465-64424479
19	MAZ	chr11:64424362-64424552	K562	blood:	n/a	n/a
20	CTCF	chr11:64424340-64424490	BE2_C	brain:	n/a	chr11:64424441-64424448
21	CTCF	chr11:64424340-64424490	HMF	breast:	n/a	chr11:64424441-64424448
22	CTCF	chr11:64424320-64424470	HPAF	blood vessel:	n/a	chr11:64424441-64424448 chr11:64424321-64424334
23	CTCF	chr11:64424360-64424510	K562	blood:	n/a	chr11:64424441-64424448
24	CTCF	chr11:64424300-64424450	GM12872	blood:	n/a	chr11:64424441-64424448 chr11:64424321-64424334
25	POLR2A	chr11:64414444-64429407	U87	brain:	n/a	n/a
26	RAD21	chr11:64424190-64424688	H1-hESC	embryonic stem cell:	n/a	chr11:64424441-64424450 chr11:64424529-64424539 chr11:64424528-64424541 chr11:64424432-64424451 chr11:64424318-64424332 chr11:64424465-64424479
27	CTCF	chr11:64424354-64424548	HepG2	liver:	n/a	chr11:64424529-64424542 chr11:64424441-64424448
28	RCOR1	chr11:64423695-64424398	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr11:64424260-64424410	HCM	heart:	n/a	chr11:64424321-64424334
30	CTCF	chr11:64424311-64424587	HepG2	liver:	n/a	chr11:64424529-64424542 chr11:64424441-64424448 chr11:64424321-64424334
31	CTCF	chr11:64424353-64424573	H1-hESC	embryonic stem cell:	n/a	chr11:64424529-64424542 chr11:64424441-64424448
32	GTF2F1	chr11:64424350-64424550	H1-hESC	embryonic stem cell:	n/a	n/a
33	NFYA	chr11:64423899-64424423	Hela-S3	cervix:	n/a	n/a
34	TFAP2A	chr11:64423534-64424399	Hela-S3	cervix:	n/a	n/a
35	TBP	chr11:64424330-64424604	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr11:64424320-64424470	AG04450	lung:	n/a	chr11:64424441-64424448 chr11:64424321-64424334
37	CTCF	chr11:64424303-64424572	K562	blood:	n/a	chr11:64424529-64424542 chr11:64424441-64424448 chr11:64424321-64424334
38	CTCF	chr11:64424240-64424510	GM12874	blood:	n/a	chr11:64424441-64424448 chr11:64424321-64424334
39	CTCF	chr11:64424217-64424677	H1-hESC	embryonic stem cell:	n/a	chr11:64424529-64424542 chr11:64424441-64424448 chr11:64424321-64424334
40	CTCF	chr11:64424253-64424645	K562	blood:	n/a	chr11:64424529-64424542 chr11:64424441-64424448 chr11:64424321-64424334
41	CTCF	chr11:64424300-64424450	AG04449	skin:	n/a	chr11:64424441-64424448 chr11:64424321-64424334
42	CTCF	chr11:64424340-64424490	WERI-Rb-1	eye:	n/a	chr11:64424441-64424448
43	SMC3	chr11:64424289-64424526	HepG2	liver:	n/a	chr11:64424324-64424334
44	CTCF	chr11:64424300-64424450	AG09319	gingival:	n/a	chr11:64424441-64424448 chr11:64424321-64424334
45	CTCF	chr11:64424340-64424490	HBMEC	blood vessel:	n/a	chr11:64424441-64424448
46	CTCF	chr11:64424360-64424510	Caco-2	colon:	n/a	chr11:64424441-64424448
47	RCOR1	chr11:64424336-64424622	K562	blood:	n/a	n/a
48	RAD21	chr11:64424289-64424576	HepG2	liver:	n/a	chr11:64424441-64424450 chr11:64424529-64424539 chr11:64424528-64424541 chr11:64424432-64424451 chr11:64424318-64424332 chr11:64424465-64424479
49	CTCF	chr11:64424240-64424390	HCM	heart:	n/a	chr11:64424321-64424334
50	CTCF	chr11:64424220-64424370	GM12873	blood:	n/a	chr11:64424321-64424334

No.	Distal block	Cell Line	Cell type
1	chr11:64423611..64425758-chr11:64437675..64439983,2	K562	blood:
2	chr11:64418565..64420140-chr11:64423624..64426189,2	K562	blood:
3	chr11:64423988..64424495-chr11:64497463..64498349,2	K562	blood:

Variant related genes	Relation type
NRXN2	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10128590	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	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897521	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]
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]
rs1207179	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1207226	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1212146	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	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]
rs2269730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285339	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361216	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957564	0.82[EUR][1000 genomes]
rs2959654	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471618	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs490192	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	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	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530775	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	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121121	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128467	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	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	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	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
rs11231848	NRXN2	cis	lung	GTEx

Chromatin state (count:62 , 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	chr11:64420400-64424800	Enhancers	Adipose Nuclei	Adipose
7	chr11:64420400-64425000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:64420400-64425200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr11:64420400-64427800	Enhancers	Fetal Thymus	thymus
10	chr11:64420600-64426600	Weak transcription	A549	lung
11	chr11:64420800-64426400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:64421000-64424800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:64421000-64425000	Weak transcription	Fetal Brain Female	brain
14	chr11:64421000-64425200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:64421000-64427200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:64421000-64434800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:64421200-64427000	Weak transcription	Brain Angular Gyrus	brain
18	chr11:64421200-64453800	Weak transcription	Fetal Brain Male	brain
19	chr11:64421400-64428600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr11:64421800-64424800	Enhancers	Placenta	Placenta
21	chr11:64422000-64425000	Enhancers	Liver	Liver
22	chr11:64422200-64424400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr11:64422200-64424600	Enhancers	Primary hematopoietic stem cells	blood
24	chr11:64422200-64424600	Enhancers	Brain Hippocampus Middle	brain
25	chr11:64422400-64427200	Weak transcription	Brain Substantia Nigra	brain
26	chr11:64422600-64424800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:64422800-64427400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr11:64423000-64424400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:64423000-64424400	Enhancers	Osteobl	bone
30	chr11:64423000-64424600	Flanking Active TSS	Hela-S3	cervix
31	chr11:64423000-64430400	Strong transcription	Brain Germinal Matrix	brain
32	chr11:64423000-64432800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:64423200-64424400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:64423200-64424400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:64423200-64424600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:64423400-64424400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:64423400-64424600	Enhancers	Fetal Muscle Leg	muscle
38	chr11:64423400-64425000	Enhancers	HSMMtube	muscle
39	chr11:64423400-64425200	Enhancers	HSMM	muscle
40	chr11:64423600-64425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:64423600-64425200	Enhancers	NHDF-Ad	bronchial
42	chr11:64423600-64427200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:64423800-64424800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr11:64423800-64426000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:64423800-64426400	Enhancers	K562	blood
46	chr11:64424000-64424400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr11:64424000-64424400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:64424000-64424400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:64424000-64424600	Enhancers	Placenta Amnion	Placenta Amnion
50	chr11:64424000-64424800	Enhancers	HUES6 Cell Line	embryonic stem cell

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