Variant report

Variant	rs1365505
Chromosome Location	chr15:50477138-50477139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr15:50477096-50477772	HepG2	liver:	n/a	n/a
2	MYBL2	chr15:50477045-50477479	HepG2	liver:	n/a	n/a
3	FOXA2	chr15:50477070-50477731	HepG2	liver:	n/a	n/a
4	SP1	chr15:50476958-50477756	HepG2	liver:	n/a	n/a
5	FOXA2	chr15:50477081-50477703	HepG2	liver:	n/a	n/a
6	ARID3A	chr15:50477121-50477623	HepG2	liver:	n/a	n/a
7	HNF4A	chr15:50477086-50477665	HepG2	liver:	n/a	chr15:50477524-50477536 chr15:50477221-50477235
8	HEY1	chr15:50477039-50477426	HepG2	liver:	n/a	n/a
9	FOXA1	chr15:50477023-50477874	HepG2	liver:	n/a	n/a
10	NFIC	chr15:50477007-50477461	HepG2	liver:	n/a	n/a
11	FOXA1	chr15:50477102-50477740	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50475267..50477449-chr15:50487507..50490048,2	K562	blood:
2	chr15:50475076..50477234-chr15:50491575..50493600,2	MCF-7	breast:
3	chr15:50471286..50473926-chr15:50475708..50479311,4	K562	blood:
4	chr15:50475880..50478806-chr15:50494358..50497931,3	MCF-7	breast:
5	chr15:50471854..50475641-chr15:50475703..50478122,4	MCF-7	breast:

No data

Variant related genes	Relation type
ATP8B4	TF binding region
ENSG00000140284	Chromatin interaction
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12164938	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1549520	0.80[LWK][hapmap];0.93[YRI][hapmap]
rs1648348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1648350	0.94[ASN][1000 genomes]
rs1797313	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1797317	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1896171	0.80[AMR][1000 genomes]
rs2052759	0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.81[AFR][1000 genomes]
rs2263561	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2554887	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28448616	0.85[AFR][1000 genomes]
rs4238381	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4775861	0.85[YRI][hapmap]
rs4775869	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7176501	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7179025	0.89[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs933856	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788756	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv904209	chr15:50444824-50482133	Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite ratios	24816252	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1365505	FRMD5	cis	parietal	SCAN
rs1365505	SLC27A2	cis	cerebellum	SCAN
rs1365505	SNORD116-27	trans	cerebellum	SCAN
rs1365505	DUOX2	cis	parietal	SCAN
rs1365505	ATP8B4	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50474200-50477400	Active TSS	Liver	Liver
2	chr15:50475800-50477600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr15:50476000-50477200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50476000-50477400	Weak transcription	Adipose Nuclei	Adipose
5	chr15:50476000-50477800	Enhancers	Duodenum Mucosa	Duodenum
6	chr15:50476000-50503400	Weak transcription	Colonic Mucosa	Colon
7	chr15:50476200-50477200	Weak transcription	Placenta	Placenta
8	chr15:50476200-50477200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:50476200-50477600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:50476200-50478200	Enhancers	Fetal Intestine Small	intestine
11	chr15:50476200-50479000	Weak transcription	K562	blood
12	chr15:50476200-50481400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:50476400-50477600	Flanking Active TSS	Hela-S3	cervix
14	chr15:50476400-50478000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr15:50476600-50498000	Weak transcription	Pancreas	Pancrea
16	chr15:50476800-50477200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:50476800-50477600	Enhancers	Fetal Intestine Large	intestine
18	chr15:50476800-50477600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr15:50477000-50477200	Flanking Active TSS	HepG2	liver
20	chr15:50477000-50477600	Enhancers	A549	lung

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