Variant report

Variant	rs2223407
Chromosome Location	chr6:167066547-167066548
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167062835..167064756-chr6:167066345..167069061,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGFR1OP-12	chr6:167064994-167067133	NONHSAT116054

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1040446	0.88[TSI][hapmap]
rs12055452	1.00[CEU][hapmap]
rs16899289	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2206124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799568	0.80[AMR][1000 genomes]
rs4145432	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes]
rs4518470	0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs58803664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60078955	0.82[EUR][1000 genomes]
rs61157638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62438677	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6933990	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs6935306	0.82[EUR][1000 genomes]
rs6937198	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs9295359	1.00[CEU][hapmap]
rs9347140	1.00[CEU][hapmap]
rs9348157	1.00[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes]
rs9348159	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9348160	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9355589	1.00[CEU][hapmap]
rs9356497	0.86[YRI][hapmap]
rs9356499	0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9356500	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs9364861	0.89[LWK][hapmap];0.86[YRI][hapmap]
rs9364863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9366036	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv432984	chr6:167018915-167181613	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1020888	chr6:167059455-167136562	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv538540	chr6:167059455-167136562	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2754464	chr6:167059528-167130749	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2223407	PHF10	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167057800-167069400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:167061600-167068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:167061800-167068800	Weak transcription	Gastric	stomach
4	chr6:167061800-167068800	Weak transcription	Pancreas	Pancrea
5	chr6:167061800-167069800	Weak transcription	Esophagus	oesophagus
6	chr6:167061800-167071000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:167061800-167071800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:167064200-167067000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:167064200-167068800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:167064200-167069400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:167064200-167069600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:167064200-167079000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:167064600-167066800	Weak transcription	Fetal Heart	heart
14	chr6:167064600-167069200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:167065400-167066600	Enhancers	Brain Germinal Matrix	brain

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