Variant report

Variant	rs17657877
Chromosome Location	chr15:41104874-41104875
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41097893..41103310-chr15:41103796..41109268,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104129	Chromatin interaction
ENSG00000166140	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10152371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070294	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070295	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070296	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070297	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]
rs11856866	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11858010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12148058	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12899910	0.81[EUR][1000 genomes]
rs12909824	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12916485	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12916535	0.95[EUR][1000 genomes]
rs17657986	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34143869	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34817886	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34948298	0.83[EUR][1000 genomes]
rs35458726	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35621205	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35853942	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736286	0.88[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743033	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743034	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4402538	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57994257	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62018585	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492967	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs690377	0.83[CHB][hapmap]
rs7178506	0.89[JPT][hapmap]
rs745032	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7915	0.83[CHB][hapmap]
rs8036842	0.81[EUR][1000 genomes]
rs8037830	0.80[AMR][1000 genomes];0.83[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17657877	RP11-111A22.1	cis	Artery Tibial	GTEx
rs17657877	C15orf57	cis	Artery Tibial	GTEx
rs17657877	ZFYVE19	cis	multi-tissue	Pritchard
rs17657877	ZFYVE19	cis	Artery Aorta	GTEx
rs17657877	CCDC32	cis	multi-tissue	Pritchard
rs17657877	ZFYVE19	cis	Thyroid	GTEx
rs17657877	ZFYVE19	cis	Nerve Tibial	GTEx
rs17657877	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs17657877	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs17657877	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs17657877	ZFYVE19	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41100200-41107600	Weak transcription	Aorta	Aorta
2	chr15:41100400-41107800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:41100600-41107800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:41100600-41108800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:41100600-41108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:41100800-41105200	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:41100800-41106000	Weak transcription	NH-A	brain
8	chr15:41100800-41107000	Weak transcription	Fetal Kidney	kidney
9	chr15:41100800-41107400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:41100800-41107600	Weak transcription	Fetal Brain Male	brain
11	chr15:41100800-41109200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:41100800-41120200	Weak transcription	Small Intestine	intestine
13	chr15:41101000-41107400	Weak transcription	Stomach Mucosa	stomach
14	chr15:41101200-41107200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:41101200-41107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:41101200-41110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:41101400-41105000	Strong transcription	Placenta	Placenta
18	chr15:41101400-41105600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:41101400-41106800	Strong transcription	Gastric	stomach
20	chr15:41101400-41107000	Strong transcription	Fetal Muscle Leg	muscle
21	chr15:41101400-41107400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr15:41101400-41107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:41101400-41107800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:41101400-41109200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:41101400-41109600	Strong transcription	Fetal Intestine Small	intestine
26	chr15:41101400-41115800	Weak transcription	A549	lung
27	chr15:41101600-41105000	Weak transcription	Brain Angular Gyrus	brain
28	chr15:41101600-41106400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:41101600-41107400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:41101600-41107400	Strong transcription	Dnd41	blood
31	chr15:41101600-41107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:41101600-41107800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:41101600-41107800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr15:41101800-41107200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:41101800-41107200	Strong transcription	Fetal Stomach	stomach
36	chr15:41101800-41107400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr15:41101800-41107400	Strong transcription	Ovary	ovary
38	chr15:41101800-41107800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:41101800-41107800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:41101800-41108000	Strong transcription	Primary T cells from cord blood	blood
41	chr15:41101800-41108200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:41101800-41108400	Strong transcription	Thymus	Thymus
43	chr15:41102000-41107200	Strong transcription	Brain Anterior Caudate	brain
44	chr15:41102000-41107600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr15:41102000-41107800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr15:41102000-41108000	Strong transcription	Fetal Thymus	thymus
47	chr15:41102000-41108200	Strong transcription	Spleen	Spleen
48	chr15:41102000-41108400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr15:41102200-41106600	Strong transcription	NHLF	lung
50	chr15:41102200-41107200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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