Variant report

Variant	rs11070297
Chromosome Location	chr15:41099349-41099350
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	CTCF	chr15:41099200-41099350	HBMEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:41098995-41099813	K562	blood:	n/a	n/a
3	JUN	chr15:41098708-41100478	K562	blood:	n/a	n/a
4	CTCF	chr15:41099320-41099470	GM12875	blood:	n/a	n/a
5	CTCF	chr15:41099300-41099450	GM12871	blood:	n/a	n/a
6	POLR2A	chr15:41099138-41100216	HepG2	liver:	n/a	n/a
7	CTCF	chr15:41099260-41099410	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr15:41098835-41100106	HCT-116	colon:	n/a	n/a
9	CTCF	chr15:41099300-41099450	HEEpiC	esophagus:	n/a	n/a
10	SMARCC2	chr15:41098940-41100619	Hela-S3	cervix:	n/a	chr15:41099667-41099676
11	TEAD4	chr15:41099026-41100330	K562	blood:	n/a	n/a
12	CTCF	chr15:41099300-41099450	HEK293	kidney:	n/a	n/a
13	ELK1	chr15:41099085-41100118	GM12878	blood:	n/a	n/a
14	GABPA	chr15:41098953-41100142	MCF-7	breast:	n/a	chr15:41099263-41099274 chr15:41099263-41099277 chr15:41099263-41099272 chr15:41099260-41099274 chr15:41099241-41099248
15	CTCF	chr15:41099240-41099390	K562	blood:	n/a	n/a
16	POLR2A	chr15:41098898-41100125	H1-neurons	neurons:	n/a	n/a
17	MAZ	chr15:41099039-41100413	Hela-S3	cervix:	n/a	chr15:41099304-41099314
18	NRF1	chr15:41099094-41099355	HepG2	liver:	n/a	chr15:41099263-41099274 chr15:41099263-41099277 chr15:41099263-41099272 chr15:41099262-41099273 chr15:41099260-41099274 chr15:41099241-41099248
19	YY1	chr15:41099062-41100277	GM12878	blood:	n/a	chr15:41099303-41099312
20	RCOR1	chr15:41099234-41100341	HepG2	liver:	n/a	n/a
21	TBP	chr15:41099047-41100435	K562	blood:	n/a	n/a
22	TCF12	chr15:41098985-41100333	ECC-1	luminal epithelium:	n/a	chr15:41100085-41100095
23	POLR2A	chr15:41099040-41100459	K562	blood:	n/a	n/a
24	ELF1	chr15:41099043-41099433	A549	lung:	n/a	n/a
25	MAX	chr15:41098859-41100205	Hela-S3	cervix:	n/a	chr15:41099304-41099314
26	PAX5	chr15:41099165-41100030	GM12892	blood:	n/a	chr15:41099748-41099766
27	TAF1	chr15:41099148-41100138	HepG2	liver:	n/a	n/a
28	SMC3	chr15:41098987-41100276	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr15:41099027-41100421	NB4	blood:	n/a	n/a
30	CREB1	chr15:41099168-41100180	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:41099315-41100155	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr15:41099285-41099938	A549	lung:	n/a	chr15:41099303-41099312
33	MAZ	chr15:41099090-41100127	GM12878	blood:	n/a	chr15:41099304-41099314
34	TCF12	chr15:41099330-41100232	ECC-1	luminal epithelium:	n/a	chr15:41100085-41100095
35	POLR2A	chr15:41098849-41100262	PFSK-1	brain:	n/a	n/a
36	CTCF	chr15:41099280-41099430	GM12875	blood:	n/a	n/a
37	SIX5	chr15:41099272-41100028	A549	lung:	n/a	chr15:41099667-41099676 chr15:41099669-41099678
38	SIN3A	chr15:41098977-41100316	H1-hESC	embryonic stem cell:	n/a	n/a
39	RCOR1	chr15:41099144-41100649	K562	blood:	n/a	n/a
40	POLR2A	chr15:41099092-41100226	HepG2	liver:	n/a	n/a
41	SIX5	chr15:41099062-41100113	A549	lung:	n/a	chr15:41099667-41099676 chr15:41099669-41099678
42	MXI1	chr15:41098950-41100285	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:41099133-41100174	A549	lung:	n/a	n/a
44	CTCF	chr15:41099041-41099851	K562	blood:	n/a	n/a
45	POLR2A	chr15:41099026-41100171	GM19193	blood:	n/a	n/a
46	CBX3	chr15:41098799-41100368	K562	blood:	n/a	n/a
47	YY1	chr15:41099209-41099434	HCT-116	colon:	n/a	chr15:41099303-41099312
48	UBTF	chr15:41099245-41099525	K562	blood:	n/a	n/a
49	TBP	chr15:41098884-41100047	GM12878	blood:	n/a	n/a
50	RCOR1	chr15:41099020-41100330	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41045748..41048901-chr15:41096709..41101394,9	K562	blood:
2	chr15:41098203..41099826-chr15:41186017..41187981,2	K562	blood:
3	chr15:41068398..41070390-chr15:41097835..41100828,2	K562	blood:
4	chr15:41053870..41057648-chr15:41097391..41099914,3	K562	blood:
5	chr15:41054213..41057951-chr15:41097645..41100150,5	K562	blood:
6	chr15:41099271..41102222-chr15:41135281..41137187,2	K562	blood:
7	chr15:41068210..41071185-chr15:41097995..41100691,2	MCF-7	breast:
8	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
9	chr15:41099333..41100176-chr9:140099690..140100435,2	Hela-S3	cervix:
10	chr15:41098099..41100613-chr15:41185742..41188181,3	K562	blood:
11	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:
12	chr15:41098827..41099580-chr18:11851185..11852024,2	Hela-S3	cervix:
13	chr15:41097893..41103310-chr15:41103796..41109268,7	MCF-7	breast:
14	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
15	chr15:41045813..41047463-chr15:41099042..41101691,3	K562	blood:

Variant related genes	Relation type
ZFYVE19	TF binding region
ENSG00000137824	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000255112	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000188566	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000187713	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10152371	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070294	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070295	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070296	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856866	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11858010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12148058	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899910	0.81[ASN][1000 genomes]
rs12909824	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12916485	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916535	0.94[EUR][1000 genomes]
rs17657877	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17657986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412567	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs34143869	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34817886	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34948298	0.82[EUR][1000 genomes]
rs35458726	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35621205	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35853942	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736286	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3743033	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4402538	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56886112	0.81[EUR][1000 genomes]
rs57818172	0.81[EUR][1000 genomes]
rs57825040	0.80[EUR][1000 genomes]
rs57943888	0.81[EUR][1000 genomes]
rs57994257	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62018585	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6492967	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs745032	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8036842	0.83[ASN][1000 genomes]
rs8037830	0.80[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv3312254	chr15:41098700-41100323	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	esv3312255	chr15:41098714-41100320	Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11070297	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs11070297	CCDC32	cis	multi-tissue	Pritchard
rs11070297	ZFYVE19	cis	Artery Tibial	GTEx
rs11070297	ZFYVE19	cis	Thyroid	GTEx
rs11070297	ZFYVE19	cis	Artery Aorta	GTEx
rs11070297	C15orf57	cis	Artery Tibial	GTEx
rs11070297	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11070297	ZFYVE19	cis	multi-tissue	Pritchard
rs11070297	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs11070297	ENSG00000166140	cis	multi-tissue	Pritchard
rs11070297	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs11070297	ZFYVE19	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41098600-41099400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr15:41098600-41099600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:41098600-41099600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:41098600-41100000	Active TSS	Rectal Smooth Muscle	rectum
5	chr15:41098600-41100600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41098600-41100600	Active TSS	A549	lung
7	chr15:41098600-41100600	Active TSS	HSMM	muscle
8	chr15:41098600-41100800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:41098800-41099400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr15:41098800-41099400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:41098800-41099400	Flanking Active TSS	HUVEC	blood vessel
12	chr15:41098800-41100200	Active TSS	Lung	lung
13	chr15:41098800-41100400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr15:41098800-41100400	Active TSS	Gastric	stomach
15	chr15:41098800-41100400	Active TSS	Pancreas	Pancrea
16	chr15:41098800-41100600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:41098800-41100600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:41098800-41100600	Active TSS	Psoas Muscle	Psoas
19	chr15:41098800-41100800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:41099000-41099400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:41099000-41100000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:41099000-41100000	Active TSS	Fetal Muscle Trunk	muscle
23	chr15:41099000-41100200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr15:41099000-41100200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:41099000-41100200	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr15:41099000-41100200	Active TSS	Aorta	Aorta
27	chr15:41099000-41100200	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr15:41099000-41100200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr15:41099000-41100400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr15:41099000-41100400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:41099000-41100400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:41099000-41100400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:41099000-41100400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:41099000-41100400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:41099000-41100400	Active TSS	Brain Hippocampus Middle	brain
36	chr15:41099000-41100400	Active TSS	Brain Substantia Nigra	brain
37	chr15:41099000-41100400	Active TSS	Colon Smooth Muscle	Colon
38	chr15:41099000-41100400	Active TSS	Esophagus	oesophagus
39	chr15:41099000-41100400	Active TSS	Left Ventricle	heart
40	chr15:41099000-41100400	Active TSS	Ovary	ovary
41	chr15:41099000-41100400	Bivalent/Poised TSS	HepG2	liver
42	chr15:41099000-41100600	Active TSS	H1 Cell Line	embryonic stem cell
43	chr15:41099000-41100600	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr15:41099000-41101000	Active TSS	NHDF-Ad	bronchial
45	chr15:41099200-41099400	Active TSS	Primary T cells fromperipheralblood	blood
46	chr15:41099200-41099400	Active TSS	Primary hematopoietic stem cells	blood
47	chr15:41099200-41099400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:41099200-41099400	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr15:41099200-41099400	Active TSS	Stomach Smooth Muscle	stomach
50	chr15:41099200-41099400	Active TSS	GM12878-XiMat	blood

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