Variant report

Variant	rs10444817
Chromosome Location	chr15:40947023-40947024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1037445	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10400890	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10400901	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070282	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070285	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070286	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632061	0.86[EUR][1000 genomes]
rs11632370	0.86[EUR][1000 genomes]
rs11852670	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852694	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852828	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854986	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855334	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855923	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11856802	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11858113	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11858938	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591207	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902568	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904801	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905162	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912635	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913697	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12914743	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16970851	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1813898	0.86[EUR][1000 genomes]
rs1967368	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2412531	0.86[EUR][1000 genomes]
rs2412532	0.86[EUR][1000 genomes]
rs2412544	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898996	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2924387	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3092979	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34845954	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35047458	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751652	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751653	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4080706	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4410047	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923876	0.86[EUR][1000 genomes]
rs4924481	0.86[EUR][1000 genomes]
rs62019916	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62019918	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582	0.86[EUR][1000 genomes]
rs71471881	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7169621	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7181074	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182530	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7183790	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026605	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8029384	0.86[EUR][1000 genomes]
rs8034043	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8034048	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036737	0.90[EUR][1000 genomes]
rs8038407	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8041534	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs896795	0.86[EUR][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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs10444817	RP11-111A22.1	cis	Stomach	GTEx
rs10444817	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs10444817	C15orf57	cis	Adipose Subcutaneous	GTEx
rs10444817	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs10444817	C15orf57	cis	Muscle Skeletal	GTEx
rs10444817	C15orf57	cis	lung	GTEx
rs10444817	C15orf57	cis	Artery Tibial	GTEx
rs10444817	C15orf57	cis	Esophagus Muscularis	GTEx
rs10444817	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs10444817	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs10444817	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs10444817	RP11-111A22.1	cis	lung	GTEx
rs10444817	C15orf57	cis	Thyroid	GTEx
rs10444817	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs10444817	C15orf57	cis	Stomach	GTEx
rs10444817	C15orf57	cis	Heart Left Ventricle	GTEx
rs10444817	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs10444817	C15orf57	cis	Artery Aorta	GTEx
rs10444817	C15orf57	cis	Nerve Tibial	GTEx
rs10444817	RP11-111A22.1	cis	Artery Aorta	GTEx
rs10444817	C15orf57	cis	Esophagus Mucosa	GTEx
rs10444817	RP11-111A22.1	cis	Artery Tibial	GTEx
rs10444817	RP11-111A22.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
6	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
9	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
10	chr15:40913800-40986000	Weak transcription	A549	lung
11	chr15:40914400-40960000	Weak transcription	NHLF	lung
12	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
14	chr15:40919800-40950200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:40922800-40954200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:40923000-40954400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:40924000-40956600	Weak transcription	Fetal Brain Female	brain
19	chr15:40925000-40956200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:40925400-40956000	Weak transcription	Brain Germinal Matrix	brain
21	chr15:40926000-40947200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:40928200-40949400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:40928200-40951200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:40934200-40949400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:40939800-40956800	Strong transcription	Dnd41	blood
28	chr15:40939800-40956800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr15:40941400-40957600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:40942000-40947400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:40942000-40947600	Strong transcription	HUVEC	blood vessel
32	chr15:40942000-40959000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:40942200-40955800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:40942400-40947600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:40942600-40955800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:40942800-40947800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:40943000-40947400	Weak transcription	Stomach Mucosa	stomach
38	chr15:40943000-40952200	Weak transcription	Fetal Intestine Small	intestine
39	chr15:40943000-40952800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:40943000-40956000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr15:40943000-40956000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
43	chr15:40943600-40947800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:40943600-40950200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:40943800-40949200	Weak transcription	Liver	Liver
46	chr15:40943800-40953800	Weak transcription	Placenta	Placenta
47	chr15:40944000-40947200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:40944200-40949400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:40944400-40949600	Weak transcription	Osteobl	bone
50	chr15:40944400-40951000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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