Variant report

Variant	rs7183790
Chromosome Location	chr15:40941898-40941899
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 24 )

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]
rs10444817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11855334	0.84[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	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11858938	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591207	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12902568	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904801	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905162	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912635	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913697	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914743	0.83[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];0.91[EUR][1000 genomes]
rs2412531	0.86[EUR][1000 genomes]
rs2412532	0.86[EUR][1000 genomes]
rs2412544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34845954	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35047458	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923876	0.86[EUR][1000 genomes]
rs4924481	0.86[EUR][1000 genomes]
rs62019916	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62019918	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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	0.84[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:24)

SNP	Gene	Cis/trans	Tissue	Source
rs7183790	C15orf57	cis	Thyroid	GTEx
rs7183790	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs7183790	CCDC32	cis	multi-tissue	Pritchard
rs7183790	C15orf57	cis	Stomach	GTEx
rs7183790	C15orf57	cis	Artery Aorta	GTEx
rs7183790	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs7183790	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs7183790	RP11-111A22.1	cis	Artery Aorta	GTEx
rs7183790	C15orf57	cis	Esophagus Mucosa	GTEx
rs7183790	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs7183790	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs7183790	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs7183790	C15orf57	cis	Artery Tibial	GTEx
rs7183790	C15orf57	cis	Nerve Tibial	GTEx
rs7183790	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs7183790	ZFYVE19	cis	multi-tissue	Pritchard
rs7183790	C15orf57	cis	Esophagus Muscularis	GTEx
rs7183790	RP11-111A22.1	cis	Stomach	GTEx
rs7183790	C15orf57	cis	Adipose Subcutaneous	GTEx
rs7183790	RP11-111A22.1	cis	Artery Tibial	GTEx
rs7183790	C15orf57	cis	lung	GTEx
rs7183790	C15orf57	cis	Heart Left Ventricle	GTEx
rs7183790	RP11-111A22.1	cis	lung	GTEx
rs7183790	C15orf57	cis	Muscle Skeletal	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
2	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40900000-40943600	Weak transcription	NH-A	brain
8	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
9	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
12	chr15:40912200-40951400	Weak transcription	Fetal Kidney	kidney
13	chr15:40913800-40986000	Weak transcription	A549	lung
14	chr15:40914400-40960000	Weak transcription	NHLF	lung
15	chr15:40914800-40942600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
18	chr15:40919800-40950200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:40922600-40943800	Weak transcription	Hela-S3	cervix
20	chr15:40922800-40944000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:40922800-40944000	Weak transcription	NHEK	skin
22	chr15:40922800-40954200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:40923000-40954400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:40923200-40947000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:40924000-40956600	Weak transcription	Fetal Brain Female	brain
27	chr15:40924400-40943600	Weak transcription	Osteobl	bone
28	chr15:40925000-40956200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:40925400-40956000	Weak transcription	Brain Germinal Matrix	brain
30	chr15:40926000-40947200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:40927200-40942000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:40928200-40949400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:40928200-40951200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:40928600-40945600	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:40931400-40944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:40932600-40946800	Weak transcription	Fetal Stomach	stomach
39	chr15:40934000-40942400	Weak transcription	NHDF-Ad	bronchial
40	chr15:40934200-40942600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:40934200-40942800	Weak transcription	HMEC	breast
42	chr15:40934200-40945000	Weak transcription	HSMM	muscle
43	chr15:40934200-40949400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:40935200-40942600	Weak transcription	K562	blood
45	chr15:40936000-40942600	Weak transcription	GM12878-XiMat	blood
46	chr15:40936200-40942000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:40936400-40943600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:40936400-40944600	Weak transcription	Thymus	Thymus
49	chr15:40938400-40942000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:40938400-40942000	Weak transcription	HUVEC	blood vessel

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