Variant report

Variant	rs2052759
Chromosome Location	chr15:50475422-50475423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:50473527-50475924	MCF-7	breast:	n/a	chr15:50474123-50474132 chr15:50474330-50474337 chr15:50474511-50474520
2	SMARCC1	chr15:50473774-50476040	Hela-S3	cervix:	n/a	n/a
3	SMC3	chr15:50474095-50476014	Hela-S3	cervix:	n/a	chr15:50474366-50474380
4	MAX	chr15:50474087-50475975	Hela-S3	cervix:	n/a	chr15:50474123-50474132 chr15:50474330-50474337 chr15:50474511-50474520
5	MYC	chr15:50474126-50475994	NB4	blood:	n/a	chr15:50474330-50474337 chr15:50474511-50474520
6	MAX	chr15:50474133-50475981	NB4	blood:	n/a	chr15:50474330-50474337 chr15:50474511-50474520
7	CUX1	chr15:50475419-50475977	K562	blood:	n/a	chr15:50475447-50475456
8	HA-E2F1	chr15:50473931-50475953	MCF-7	breast:	n/a	chr15:50474373-50474382
9	RCOR1	chr15:50474129-50476016	Hela-S3	cervix:	n/a	n/a
10	RFX5	chr15:50474218-50475961	Hela-S3	cervix:	n/a	chr15:50474408-50474417
11	GTF2F1	chr15:50474908-50475987	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:50473723-50475990	Hela-S3	cervix:	n/a	n/a
13	ELF1	chr15:50473606-50476198	MCF-7	breast:	n/a	chr15:50474375-50474387 chr15:50474439-50474451
14	RCOR1	chr15:50475407-50476181	K562	blood:	n/a	n/a
15	POLR2A	chr15:50474139-50476125	Hela-S3	cervix:	n/a	n/a
16	HDAC2	chr15:50473644-50476019	MCF-7	breast:	n/a	n/a
17	MXI1	chr15:50474135-50475997	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr15:50474226-50475997	Hela-S3	cervix:	n/a	chr15:50474366-50474380 chr15:50474365-50474384

No.	Distal block	Cell Line	Cell type
1	chr15:50475267..50477449-chr15:50487507..50490048,2	K562	blood:
2	chr15:50473541..50475661-chr15:50496786..50499425,2	MCF-7	breast:
3	chr15:50475076..50477234-chr15:50491575..50493600,2	MCF-7	breast:
4	chr15:50473948..50476834-chr15:50511893..50514231,2	MCF-7	breast:
5	chr15:50471646..50476620-chr15:50646050..50650091,9	MCF-7	breast:
6	chr15:50473235..50476211-chr15:50645559..50648841,7	MCF-7	breast:

Variant related genes	Relation type
ATP8B4	TF binding region
ENSG00000104064	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000200605	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1365505	0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.81[AFR][1000 genomes]
rs1549520	0.84[LWK][hapmap]
rs1648348	0.82[JPT][hapmap];0.83[AFR][1000 genomes]
rs1797317	0.84[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs1797319	0.83[EUR][1000 genomes]
rs2433283	0.89[MEX][hapmap];0.84[EUR][1000 genomes]
rs2555487	0.83[EUR][1000 genomes]
rs2899458	0.84[EUR][1000 genomes]
rs4238381	0.82[JPT][hapmap]
rs6493415	0.84[EUR][1000 genomes]
rs7176501	0.81[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap]
rs7179025	0.89[LWK][hapmap]
rs933856	0.88[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap]
rs933857	0.89[MEX][hapmap];0.84[EUR][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2052759	SLC27A2	cis	parietal	SCAN
rs2052759	MLF1IP	trans	cerebellum	SCAN
rs2052759	ATP8B4	cis	cerebellar cortex	BrainEAC
rs2052759	ATP8B4	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50473600-50475600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr15:50473800-50475600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:50473800-50475800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:50474000-50475600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:50474000-50475800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr15:50474000-50476000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr15:50474000-50476000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
8	chr15:50474000-50476000	Bivalent/Poised TSS	Fetal Kidney	kidney
9	chr15:50474000-50476000	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr15:50474000-50476200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:50474200-50477400	Active TSS	Liver	Liver
12	chr15:50474400-50475600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:50474600-50475600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
14	chr15:50474600-50475800	Flanking Active TSS	Pancreas	Pancrea
15	chr15:50474800-50475800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr15:50474800-50476000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:50475000-50475600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
18	chr15:50475000-50475600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:50475000-50475600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr15:50475000-50475800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
21	chr15:50475000-50475800	Bivalent Enhancer	Fetal Heart	heart
22	chr15:50475000-50475800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
23	chr15:50475000-50476000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:50475000-50476000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:50475000-50476000	Flanking Active TSS	K562	blood
26	chr15:50475200-50475600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
27	chr15:50475200-50475600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
28	chr15:50475200-50475600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
29	chr15:50475200-50475600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr15:50475200-50475600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr15:50475200-50475600	Active TSS	Fetal Intestine Small	intestine
32	chr15:50475200-50475600	Enhancers	Fetal Thymus	thymus
33	chr15:50475200-50475800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:50475200-50475800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr15:50475200-50475800	Enhancers	Gastric	stomach
36	chr15:50475200-50475800	Bivalent Enhancer	Stomach Mucosa	stomach
37	chr15:50475200-50476000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:50475200-50476000	Active TSS	Colonic Mucosa	Colon
39	chr15:50475200-50476000	Flanking Active TSS	A549	lung
40	chr15:50475200-50476000	Flanking Active TSS	HepG2	liver
41	chr15:50475200-50476200	Active TSS	Placenta	Placenta
42	chr15:50475400-50475600	Enhancers	Primary B cells from cord blood	blood
43	chr15:50475400-50475600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr15:50475400-50475600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:50475400-50475600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:50475400-50475600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
47	chr15:50475400-50475600	Enhancers	Esophagus	oesophagus
48	chr15:50475400-50475600	Bivalent Enhancer	Fetal Brain Female	brain
49	chr15:50475400-50475600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
50	chr15:50475400-50475600	Bivalent Enhancer	GM12878-XiMat	blood

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