Variant report

Variant	rs59739006
Chromosome Location	chr11:64415903-64415904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64415362-64419245	U87	brain:	n/a	n/a
2	POLR2A	chr11:64411167-64429413	U87	brain:	n/a	n/a
3	POLR2A	chr11:64415650-64416410	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr11:64415198-64418364	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr11:64414444-64429407	U87	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64221626..64223202-chr11:64414633..64417445,2	K562	blood:
2	chr11:64083939..64086928-chr11:64415320..64417801,2	K562	blood:
3	chr11:64406905..64410003-chr11:64415676..64418425,3	K562	blood:
4	chr11:64410404..64412762-chr11:64414408..64417376,3	MCF-7	breast:
5	chr11:64256962..64257955-chr11:64415412..64417537,12	MCF-7	breast:
6	chr11:64268201..64270623-chr11:64415596..64417304,2	K562	blood:

No data

Variant related genes	Relation type
NRXN2	TF binding region
ENSG00000173113	Chromatin interaction
ENSG00000110076	Chromatin interaction
ENSG00000232500	Chromatin interaction
ENSG00000126432	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11602411	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12273892	0.84[ASN][1000 genomes]
rs2022050	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2666558	0.84[ASN][1000 genomes]
rs2666560	0.81[ASN][1000 genomes]
rs3825074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478607	0.84[ASN][1000 genomes]
rs521793	0.84[ASN][1000 genomes]
rs551890	0.84[ASN][1000 genomes]
rs60159753	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61884374	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884411	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61884413	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61884449	0.82[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
rs59739006	NRXN2	cis	lung	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64411600-64427800	Weak transcription	Aorta	Aorta
2	chr11:64411800-64416800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:64411800-64420000	Weak transcription	Brain Substantia Nigra	brain
4	chr11:64411800-64420200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:64411800-64420400	Weak transcription	Brain Angular Gyrus	brain
6	chr11:64412000-64416400	Weak transcription	Ovary	ovary
7	chr11:64412200-64416800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:64412400-64428200	Weak transcription	Right Atrium	heart
9	chr11:64412600-64419800	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:64412600-64420000	Weak transcription	Brain Anterior Caudate	brain
11	chr11:64412600-64425600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:64412800-64416600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:64413000-64420000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:64413600-64416200	Strong transcription	Fetal Brain Female	brain
15	chr11:64413800-64416000	Enhancers	Fetal Muscle Leg	muscle
16	chr11:64413800-64416000	Enhancers	Spleen	Spleen
17	chr11:64414000-64416800	Weak transcription	Fetal Thymus	thymus
18	chr11:64414400-64416200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
19	chr11:64414400-64418800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr11:64414600-64416000	Bivalent Enhancer	Fetal Stomach	stomach
21	chr11:64414600-64417000	Enhancers	HSMMtube	muscle
22	chr11:64415000-64418000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr11:64415000-64423600	Weak transcription	NHDF-Ad	bronchial
24	chr11:64415400-64416200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:64415400-64416800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr11:64415400-64423000	Weak transcription	Osteobl	bone
27	chr11:64415600-64420200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:64415600-64420400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:64415600-64422400	Weak transcription	HSMM	muscle
30	chr11:64415600-64423000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:64415800-64418000	Weak transcription	Brain Germinal Matrix	brain
32	chr11:64415800-64430000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links