Variant report

Variant	rs17748059
Chromosome Location	chr15:42380802-42380803
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42363019..42364718-chr15:42379292..42382030,2	K562	blood:
2	chr15:42370010..42372757-chr15:42379600..42382035,2	K562	blood:
3	chr15:42378120..42380874-chr15:42393384..42396333,2	K562	blood:

Variant related genes	Relation type
ENSG00000159337	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12148416	0.87[EUR][1000 genomes]
rs17690109	0.91[CEU][hapmap]
rs17690827	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17690899	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17691153	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17691880	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17747505	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17748132	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17748317	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2412656	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35200589	0.86[EUR][1000 genomes]
rs4923923	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4923924	0.87[EUR][1000 genomes]
rs4923925	0.87[EUR][1000 genomes]
rs4923926	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923927	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923928	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924609	0.84[CEU][hapmap];0.91[GIH][hapmap]
rs4924611	0.92[CEU][hapmap]
rs4924614	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924615	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924616	0.87[EUR][1000 genomes]
rs4924617	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4924619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924620	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7162019	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165460	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166026	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7166093	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7166111	1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7166789	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168863	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173686	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7176443	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7177034	0.82[CEU][hapmap]
rs7180420	0.87[EUR][1000 genomes]
rs750051	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs750052	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs755599	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs8029713	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042953	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv436201	chr15:42380264-42387429	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17748059	RTF1	cis	parietal	SCAN
rs17748059	CATSPER2P1	cis	parietal	SCAN
rs17748059	IVD	cis	parietal	SCAN
rs17748059	GPR176	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42369800-42385000	Weak transcription	Right Atrium	heart
2	chr15:42372800-42383000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:42373400-42384400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:42373400-42384400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:42376800-42384400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:42377000-42381000	Weak transcription	Fetal Heart	heart
7	chr15:42377200-42381200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:42377400-42381000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:42377400-42382400	Weak transcription	Fetal Intestine Large	intestine
10	chr15:42377400-42384800	Weak transcription	Esophagus	oesophagus
11	chr15:42377600-42381000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:42377600-42381400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:42377600-42383000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:42377600-42384800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:42377800-42382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:42377800-42384200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:42378000-42381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:42378000-42382400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:42378000-42382400	Weak transcription	NHEK	skin
20	chr15:42378200-42382600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:42378200-42382600	Weak transcription	HMEC	breast
22	chr15:42378200-42384800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:42380000-42381400	Enhancers	Hela-S3	cervix
24	chr15:42380000-42383000	Enhancers	Stomach Mucosa	stomach
25	chr15:42380200-42381600	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr15:42380200-42383000	Enhancers	Gastric	stomach
27	chr15:42380800-42381600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr15:42380800-42381600	Enhancers	Fetal Thymus	thymus
29	chr15:42380800-42382200	Enhancers	Pancreas	Pancrea

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