Variant report

Variant	rs7148240
Chromosome Location	chr14:80041744-80041745
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10137102	0.86[ASW][hapmap];0.89[YRI][hapmap]
rs10148779	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[ASN][1000 genomes]
rs1364604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364606	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544726	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544842	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17109500	0.89[YRI][hapmap]
rs17764137	0.87[ASN][1000 genomes]
rs2371058	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59300744	0.95[ASN][1000 genomes]
rs7141526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154918	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7156216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7160334	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73326050	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323674	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9652379	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045241	chr14:79885361-80734201	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1039622	chr14:79908702-80266601	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv902112	chr14:79939393-80050771	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv869542	chr14:80009619-80118315	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7148240	NRXN3	cis	cerebellum	SCAN
rs7148240	C14orf174	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:80011800-80069200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr14:80037000-80044600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr14:80038000-80042000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr14:80038000-80042200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr14:80038000-80042400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:80038000-80043400	Weak transcription	Aorta	Aorta
7	chr14:80038600-80042200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr14:80039200-80043200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr14:80039800-80046200	Weak transcription	HSMMtube	muscle
10	chr14:80040000-80049400	Weak transcription	HSMM	muscle
11	chr14:80040200-80042800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:80040600-80043000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr14:80041000-80042800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr14:80041000-80043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:80041200-80041800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr14:80041200-80041800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr14:80041200-80042000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr14:80041200-80042000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr14:80041200-80042200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:80041400-80042200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr14:80041400-80042200	Weak transcription	Fetal Lung	lung
22	chr14:80041600-80041800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:80041600-80044800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:80041600-80044800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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