Variant report

Variant	rs7156216
Chromosome Location	chr14:80042924-80042925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10134188	0.82[AFR][1000 genomes]
rs10137102	0.86[ASW][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap]
rs10148779	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs1364604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1364606	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544726	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1544842	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17109500	0.89[YRI][hapmap]
rs17764137	0.85[ASN][1000 genomes]
rs2371058	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59300744	0.93[ASN][1000 genomes]
rs61153207	0.80[AFR][1000 genomes]
rs7141526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7148240	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]
rs7154918	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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];0.84[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73326053	0.81[AFR][1000 genomes]
rs9323674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652379	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[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
rs7156216	NRXN3	cis	cerebellum	SCAN
rs7156216	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	chr14:80038000-80043400	Weak transcription	Aorta	Aorta
4	chr14:80039200-80043200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr14:80039800-80046200	Weak transcription	HSMMtube	muscle
6	chr14:80040000-80049400	Weak transcription	HSMM	muscle
7	chr14:80040600-80043000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr14:80041000-80043000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:80041600-80044800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr14:80041600-80044800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr14:80041800-80046600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:80042000-80044200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:80042200-80043000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:80042200-80043000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr14:80042200-80043400	Enhancers	Fetal Muscle Leg	muscle
16	chr14:80042200-80043600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr14:80042200-80051200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:80042400-80043000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:80042600-80043000	Bivalent Enhancer	Fetal Brain Male	brain
20	chr14:80042600-80043000	Enhancers	NH-A	brain
21	chr14:80042800-80043000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr14:80042800-80043000	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr14:80042800-80043200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr14:80042800-80044600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links