Variant report

Variant	rs4714144
Chromosome Location	chr6:38273091-38273092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38269604..38272894-chr6:38272996..38276303,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1475761	0.96[CEU][hapmap]
rs1931767	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs228181	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs228182	0.96[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs228184	0.91[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs228185	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs228187	0.96[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs4711533	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4714136	0.95[CEU][hapmap]
rs4714140	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6905637	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922620	0.95[CEU][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7760807	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349067	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380737	0.87[CEU][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs9470847	0.96[CEU][hapmap]
rs9470848	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs9470850	0.96[LWK][hapmap];0.91[YRI][hapmap]
rs9470851	0.96[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9470856	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4714144	SPTLC3	trans	lymphoblastoid	RTeQTL
rs4714144	C6orf106	cis	parietal	SCAN
rs4714144	C6orf64	cis	cerebellum	SCAN
rs4714144	C6orf129	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38249200-38275600	Weak transcription	Fetal Brain Male	brain
2	chr6:38267400-38274000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:38270200-38275400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:38270800-38274000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:38270800-38275600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:38271000-38275000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:38271200-38275600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:38271400-38274600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:38272600-38273600	Enhancers	GM12878-XiMat	blood

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