Variant report

Variant	rs2412567
Chromosome Location	chr15:41103862-41103863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];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	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070296	0.92[CEU][hapmap];0.82[JPT][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];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]
rs17657877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657986	1.00[CEU][hapmap];0.87[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
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	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3743033	0.92[CEU][hapmap];0.82[JPT][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];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	0.82[CHB][hapmap]
rs7178506	0.89[JPT][hapmap]
rs745032	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7915	0.82[CHB][hapmap]
rs8036842	0.81[EUR][1000 genomes]
rs8037830	0.84[CEU][hapmap];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
rs2412567	ZFYVE19	cis	Nerve Tibial	GTEx
rs2412567	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs2412567	ZFYVE19	cis	Artery Aorta	GTEx
rs2412567	C15orf57	cis	Artery Tibial	GTEx
rs2412567	ZFYVE19	cis	Esophagus Muscularis	GTEx
rs2412567	ZFYVE19	cis	Artery Tibial	GTEx
rs2412567	ZFYVE19	cis	Thyroid	GTEx
rs2412567	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2412567	CCDC32	cis	multi-tissue	Pritchard
rs2412567	ZFYVE19	cis	multi-tissue	Pritchard
rs2412567	RP11-111A22.1	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 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	chr15:41100600-41104600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:41100600-41107800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:41100600-41108800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:41100600-41108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:41100800-41104200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:41100800-41105200	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:41100800-41106000	Weak transcription	NH-A	brain
10	chr15:41100800-41107000	Weak transcription	Fetal Kidney	kidney
11	chr15:41100800-41107400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:41100800-41107600	Weak transcription	Fetal Brain Male	brain
13	chr15:41100800-41109200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:41100800-41120200	Weak transcription	Small Intestine	intestine
15	chr15:41101000-41104800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:41101000-41107400	Weak transcription	Stomach Mucosa	stomach
17	chr15:41101200-41107200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:41101200-41107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:41101200-41110400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:41101400-41105000	Strong transcription	Placenta	Placenta
21	chr15:41101400-41105600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:41101400-41106800	Strong transcription	Gastric	stomach
23	chr15:41101400-41107000	Strong transcription	Fetal Muscle Leg	muscle
24	chr15:41101400-41107400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr15:41101400-41107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:41101400-41107800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:41101400-41109200	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:41101400-41109600	Strong transcription	Fetal Intestine Small	intestine
29	chr15:41101400-41115800	Weak transcription	A549	lung
30	chr15:41101600-41105000	Weak transcription	Brain Angular Gyrus	brain
31	chr15:41101600-41106400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:41101600-41107400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:41101600-41107400	Strong transcription	Dnd41	blood
34	chr15:41101600-41107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:41101600-41107800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:41101600-41107800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr15:41101800-41104600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:41101800-41104800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:41101800-41107200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:41101800-41107200	Strong transcription	Fetal Stomach	stomach
41	chr15:41101800-41107400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr15:41101800-41107400	Strong transcription	Ovary	ovary
43	chr15:41101800-41107800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:41101800-41107800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:41101800-41108000	Strong transcription	Primary T cells from cord blood	blood
46	chr15:41101800-41108200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:41101800-41108400	Strong transcription	Thymus	Thymus
48	chr15:41102000-41107200	Strong transcription	Brain Anterior Caudate	brain
49	chr15:41102000-41107600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr15:41102000-41107800	Strong transcription	Monocytes-CD14+_RO01746	blood

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