Variant report

Variant	rs11070296
Chromosome Location	chr15:41098354-41098355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr15:41098216-41098394	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

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	chr15:41068210..41071185-chr15:41097995..41100691,2	MCF-7	breast:
7	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
8	chr15:41098099..41100613-chr15:41185742..41188181,3	K562	blood:
9	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:
10	chr15:41097893..41103310-chr15:41103796..41109268,7	MCF-7	breast:

No data

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

Extended variants
information (count: 43 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10152371	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070294	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070297	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	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858010	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12148058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899910	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12905621	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12909824	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916485	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916535	0.85[EUR][1000 genomes]
rs17657877	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17657986	0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2010300	0.84[CEU][hapmap];0.83[MEX][hapmap]
rs2289219	0.84[CEU][hapmap]
rs2412567	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs2899000	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs34143869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34817886	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34948298	0.90[EUR][1000 genomes]
rs35458726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35621205	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35853942	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3736286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743034	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4402538	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56886112	0.88[EUR][1000 genomes]
rs57818172	0.88[EUR][1000 genomes]
rs57825040	0.88[EUR][1000 genomes]
rs57943888	0.88[EUR][1000 genomes]
rs57994257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62018584	0.81[EUR][1000 genomes]
rs62018585	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492967	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745032	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8036842	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8037830	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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	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

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs11070296	ZFYVE19	cis	cerebellum	SCAN
rs11070296	ZFYVE19	cis	lymphoblastoid	seeQTL
rs11070296	AK026378	trans	multi-tissue	Pritchard
rs11070296	ZFYVE19	cis	parietal	SCAN
rs11070296	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs11070296	RHOV	cis	multi-tissue	Pritchard
rs11070296	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs11070296	ZFYVE19	cis	Artery Aorta	GTEx
rs11070296	ZFYVE19	cis	Artery Tibial	GTEx
rs11070296	C15orf57	cis	Adipose Subcutaneous	GTEx
rs11070296	C15orf57	cis	cerebellum	SCAN
rs11070296	CCDC32	cis	multi-tissue	Pritchard
rs11070296	ZFYVE19	cis	Nerve Tibial	GTEx
rs11070296	ZFYVE19	cis	multi-tissue	Pritchard
rs11070296	ZFYVE19	cis	Thyroid	GTEx
rs11070296	C15orf57	cis	parietal	SCAN
rs11070296	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs11070296	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11070296	C15orf57	cis	Artery Tibial	GTEx
rs11070296	C15orf23	cis	cerebellum	SCAN
rs11070296	C15orf57	cis	lymphoblastoid	seeQTL
rs11070296	ZFYVE19	cis	Liver	GTEx
rs11070296	THBS1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41072600-41098600	Weak transcription	Fetal Brain Female	brain
2	chr15:41072600-41098600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:41078200-41098600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41079600-41098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41080000-41099000	Weak transcription	Aorta	Aorta
6	chr15:41080400-41098600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:41080400-41098800	Weak transcription	Brain Angular Gyrus	brain
8	chr15:41080400-41098800	Weak transcription	Brain Anterior Caudate	brain
9	chr15:41080600-41098600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:41080600-41098600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:41080600-41098600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr15:41082000-41098600	Weak transcription	Fetal Lung	lung
13	chr15:41082000-41098800	Weak transcription	Fetal Kidney	kidney
14	chr15:41086000-41098600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:41086000-41098600	Weak transcription	Primary B cells from cord blood	blood
16	chr15:41086000-41098800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:41086000-41098800	Weak transcription	Esophagus	oesophagus
18	chr15:41086200-41098400	Weak transcription	K562	blood
19	chr15:41086200-41098600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:41086200-41098600	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:41086200-41098600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:41086200-41098600	Weak transcription	Brain Substantia Nigra	brain
23	chr15:41086200-41098600	Weak transcription	HSMM	muscle
24	chr15:41086200-41098600	Weak transcription	NH-A	brain
25	chr15:41086200-41098600	Weak transcription	Osteobl	bone
26	chr15:41086200-41098800	Weak transcription	HSMMtube	muscle
27	chr15:41086200-41098800	Weak transcription	NHDF-Ad	bronchial
28	chr15:41086400-41098600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:41087800-41098600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:41089200-41098800	Weak transcription	Small Intestine	intestine
31	chr15:41089400-41098600	Weak transcription	Colonic Mucosa	Colon
32	chr15:41089400-41098600	Weak transcription	HUVEC	blood vessel
33	chr15:41089600-41098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:41089600-41098800	Weak transcription	HMEC	breast
35	chr15:41091000-41098600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:41091000-41098600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:41091000-41098600	Weak transcription	A549	lung
38	chr15:41091000-41098800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:41091600-41098800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:41091800-41098600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:41092000-41098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:41092000-41098800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:41092000-41098800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:41092200-41098800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:41092200-41098800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:41092200-41098800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:41092400-41098800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:41093600-41098600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:41094200-41098600	Weak transcription	Placenta	Placenta
50	chr15:41094400-41098800	Weak transcription	Right Atrium	heart

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