Variant report

Variant	rs7160334
Chromosome Location	chr14:80034865-80034866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10132897	0.84[AFR][1000 genomes]
rs10134188	0.88[AFR][1000 genomes]
rs10137102	0.92[ASW][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs10148779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10149978	0.81[YRI][hapmap]
rs1364604	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1364606	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544726	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544842	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17109500	0.85[ASW][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs17764137	0.89[ASN][1000 genomes]
rs2371058	1.00[EUR][1000 genomes]
rs28519457	0.80[AFR][1000 genomes]
rs28584086	0.84[AFR][1000 genomes]
rs59300744	0.93[ASN][1000 genomes]
rs61153207	0.89[AFR][1000 genomes]
rs7141526	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7148240	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]
rs7154918	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7156216	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];0.84[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73326050	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73326053	0.89[AFR][1000 genomes]
rs73326059	0.87[AFR][1000 genomes]
rs9323674	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652379	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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
rs7160334	C14orf174	cis	cerebellum	SCAN
rs7160334	NRXN3	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:80011800-80069200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr14:80014400-80037800	Weak transcription	Aorta	Aorta
3	chr14:80027600-80036600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:80033400-80036000	Enhancers	Brain Hippocampus Middle	brain
5	chr14:80033800-80035800	Enhancers	Brain Germinal Matrix	brain
6	chr14:80034200-80036200	Enhancers	Brain Substantia Nigra	brain
7	chr14:80034400-80035600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr14:80034400-80035600	Enhancers	Brain Cingulate Gyrus	brain
9	chr14:80034400-80035800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr14:80034400-80035800	Enhancers	Brain Angular Gyrus	brain
11	chr14:80034400-80035800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr14:80034600-80035400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr14:80034600-80035600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr14:80034600-80035800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:80034800-80035600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr14:80034800-80035600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr14:80034800-80035600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr14:80034800-80035800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr14:80034800-80035800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr14:80034800-80035800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:80034800-80038200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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