Variant report

Variant	rs12431444
Chromosome Location	chr14:42068689-42068690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10131184	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs10140527	0.96[CEU][hapmap];0.96[TSI][hapmap]
rs10483526	0.93[EUR][1000 genomes]
rs1111177	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1111179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11157240	0.85[EUR][1000 genomes]
rs11157241	0.91[EUR][1000 genomes]
rs11157242	0.88[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs1117723	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs1137567	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs12100476	0.84[JPT][hapmap]
rs12100840	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12100891	0.84[JPT][hapmap]
rs12589043	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12589112	0.90[ASN][1000 genomes]
rs1609735	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112133	0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs17112137	0.87[ASN][1000 genomes]
rs17781288	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs1950831	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1950834	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1950835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1950836	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1950838	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1956446	0.84[JPT][hapmap]
rs1956447	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1956450	0.93[EUR][1000 genomes]
rs1998126	0.87[ASN][1000 genomes]
rs2121708	0.85[EUR][1000 genomes]
rs28755010	0.86[ASN][1000 genomes]
rs2899928	0.88[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs4356390	0.97[EUR][1000 genomes]
rs58845274	0.90[ASN][1000 genomes]
rs61990286	0.98[EUR][1000 genomes]
rs61990288	0.98[EUR][1000 genomes]
rs61990289	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6572097	0.84[JPT][hapmap]
rs6572099	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7148091	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72684563	0.92[EUR][1000 genomes]
rs8003822	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8007172	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8013655	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047300	chr14:41671653-42361098	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831164	chr14:41673017-42103168	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv533968	chr14:41882101-42327882	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1042078	chr14:41993985-42120143	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758353	chr14:42045873-42259511	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2759983	chr14:42045873-42259511	ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12431444	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:42056800-42069200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:42067000-42074000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:42067200-42073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:42067200-42073800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:42067400-42073600	Weak transcription	Placenta	Placenta
6	chr14:42067600-42069400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr14:42067800-42069400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr14:42068200-42068800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr14:42068400-42068800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr14:42068400-42068800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr14:42068400-42069000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr14:42068400-42069800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr14:42068400-42071400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr14:42068600-42069600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr14:42068600-42069600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr14:42068600-42069600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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