Variant report

Variant	rs502567
Chromosome Location	chr11:64419218-64419219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64216070..64217307-chr11:64418059..64419748,6	MCF-7	breast:
2	chr11:64418565..64420140-chr11:64423624..64426189,2	K562	blood:
3	chr11:64125161..64127762-chr11:64418891..64421292,2	MCF-7	breast:
4	chr11:64419216..64421047-chr11:64455439..64457519,3	MCF-7	breast:
5	chr11:64417046..64419414-chr11:64442413..64444571,2	MCF-7	breast:
6	chr11:64320724..64321708-chr11:64418720..64419512,2	MCF-7	breast:
7	chr11:64298941..64300555-chr11:64417105..64419761,2	K562	blood:

Variant related genes	Relation type
ENSG00000181908	Chromatin interaction
ENSG00000162302	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10128590	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10792445	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10897519	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10897521	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231837	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231838	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231848	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11605121	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1207179	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1207226	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1212146	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12269736	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17146216	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2022051	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269730	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285339	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2361216	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2957564	0.81[AMR][1000 genomes]
rs2959654	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs471618	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs490192	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs506035	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs516117	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530252	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530775	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs557709	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55908793	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56105921	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61884406	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7117423	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7121121	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7128467	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72927012	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7929296	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7929627	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7932775	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7937990	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs948689	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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
rs502567	NRXN2	cis	lung	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64411600-64427800	Weak transcription	Aorta	Aorta
2	chr11:64411800-64420000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:64411800-64420200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:64411800-64420400	Weak transcription	Brain Angular Gyrus	brain
5	chr11:64412400-64428200	Weak transcription	Right Atrium	heart
6	chr11:64412600-64419800	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:64412600-64420000	Weak transcription	Brain Anterior Caudate	brain
8	chr11:64412600-64425600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:64413000-64420000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:64415000-64423600	Weak transcription	NHDF-Ad	bronchial
11	chr11:64415400-64423000	Weak transcription	Osteobl	bone
12	chr11:64415600-64420200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:64415600-64420400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:64415600-64422400	Weak transcription	HSMM	muscle
15	chr11:64415600-64423000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:64415800-64430000	Weak transcription	Gastric	stomach
17	chr11:64417000-64420800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:64417000-64420800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:64417000-64422600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:64417000-64423400	Weak transcription	HSMMtube	muscle
21	chr11:64417200-64419600	Weak transcription	Fetal Intestine Large	intestine
22	chr11:64417200-64419800	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:64417200-64420200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:64417200-64420400	Weak transcription	Ovary	ovary
25	chr11:64417200-64420400	Weak transcription	Spleen	Spleen
26	chr11:64417200-64421200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:64417400-64420400	Weak transcription	Fetal Thymus	thymus
28	chr11:64418000-64419800	Strong transcription	Brain Germinal Matrix	brain
29	chr11:64418400-64419600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr11:64418400-64420400	Weak transcription	Pancreas	Pancrea
31	chr11:64418600-64419600	Strong transcription	Fetal Muscle Leg	muscle
32	chr11:64418600-64421200	Enhancers	Fetal Intestine Small	intestine
33	chr11:64418800-64420200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:64418800-64420200	Weak transcription	Fetal Lung	lung
35	chr11:64418800-64420400	Weak transcription	Fetal Brain Female	brain
36	chr11:64418800-64420600	Weak transcription	Right Ventricle	heart
37	chr11:64418800-64420800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:64419000-64420400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:64419200-64419600	Weak transcription	K562	blood

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