Variant report

Variant	rs62317868
Chromosome Location	chr4:129725180-129725181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10017436	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11098987	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724119	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1425618	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1648062	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs167618	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17013778	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2016294	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs318504	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318505	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs318555	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs318556	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4975263	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975264	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975266	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975268	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975270	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55829553	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833391	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844446	0.87[EUR][1000 genomes];0.86[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv822717	chr4:129724785-129739862	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62317868	PHF17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129719800-129726200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr4:129720000-129726400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:129721600-129725400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr4:129723600-129730000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:129723600-129730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:129724000-129726200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr4:129724200-129725200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr4:129724200-129725200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:129724200-129725600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr4:129724200-129725600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:129724200-129725600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:129724200-129725600	Enhancers	Fetal Intestine Small	intestine
13	chr4:129724200-129726200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr4:129724400-129725200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:129724400-129725400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:129724400-129725400	Enhancers	Stomach Mucosa	stomach
17	chr4:129724400-129726200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:129724400-129726200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:129724400-129727400	Enhancers	Placenta	Placenta
20	chr4:129724600-129725200	Active TSS	Colonic Mucosa	Colon
21	chr4:129724600-129725400	Enhancers	Duodenum Mucosa	Duodenum
22	chr4:129724600-129725600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:129724600-129725600	Enhancers	Fetal Intestine Large	intestine
24	chr4:129724600-129726200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:129724600-129726200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:129724800-129725200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr4:129724800-129725200	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr4:129724800-129725200	Flanking Active TSS	GM12878-XiMat	blood
29	chr4:129724800-129725400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr4:129724800-129725400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr4:129724800-129725400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:129724800-129725600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr4:129724800-129726200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr4:129724800-129726400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:129724800-129726400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr4:129724800-129730600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:129725000-129725200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:129725000-129725400	Enhancers	K562	blood
39	chr4:129725000-129730400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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