Variant report

Variant	rs8038396
Chromosome Location	chr15:40957370-40957371
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1051482	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851396	0.86[EUR][1000 genomes]
rs11070279	0.87[EUR][1000 genomes]
rs11070280	0.87[EUR][1000 genomes]
rs11070290	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11852479	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11855517	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12148185	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898552	0.87[AMR][1000 genomes]
rs12899408	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12906755	0.97[EUR][1000 genomes]
rs12907448	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907984	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12908114	0.87[EUR][1000 genomes]
rs12908443	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908867	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12910784	0.80[AMR][1000 genomes]
rs12914501	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12915563	0.85[EUR][1000 genomes]
rs1453183	0.86[EUR][1000 genomes]
rs17746659	0.87[EUR][1000 genomes]
rs17747399	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304583	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2412545	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28798094	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34303240	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34750756	0.85[EUR][1000 genomes]
rs35884042	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36094699	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3743146	0.85[EUR][1000 genomes]
rs3803353	0.84[EUR][1000 genomes]
rs4457966	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45592734	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5030783	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55954396	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56384845	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62019866	0.84[EUR][1000 genomes]
rs62019883	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62019934	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7162749	0.85[EUR][1000 genomes]
rs7165054	0.85[EUR][1000 genomes]
rs8025458	0.85[EUR][1000 genomes]
rs8031427	0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8036938	0.84[EUR][1000 genomes]
rs8042733	0.84[EUR][1000 genomes]
rs9806410	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs8038396	C15orf57	cis	lung	GTEx
rs8038396	RP11-111A22.1	cis	lung	GTEx
rs8038396	C15orf57	cis	Stomach	GTEx
rs8038396	C15orf57	cis	Artery Aorta	GTEx
rs8038396	RP11-111A22.1	cis	Stomach	GTEx
rs8038396	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs8038396	C15orf57	cis	Esophagus Muscularis	GTEx
rs8038396	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs8038396	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs8038396	RP11-111A22.1	cis	Artery Tibial	GTEx
rs8038396	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs8038396	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs8038396	RP11-111A22.1	cis	Artery Aorta	GTEx
rs8038396	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs8038396	C15orf57	cis	Adipose Subcutaneous	GTEx
rs8038396	C15orf57	cis	Artery Tibial	GTEx
rs8038396	C15orf57	cis	Nerve Tibial	GTEx
rs8038396	C15orf57	cis	Esophagus Mucosa	GTEx
rs8038396	C15orf57	cis	Muscle Skeletal	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:40913800-40986000	Weak transcription	A549	lung
3	chr15:40914400-40960000	Weak transcription	NHLF	lung
4	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:40941400-40957600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:40942000-40959000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
10	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:40945200-40961400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:40946600-40957600	Weak transcription	HSMM	muscle
13	chr15:40946600-40957600	Weak transcription	NH-A	brain
14	chr15:40946600-40959800	Weak transcription	Gastric	stomach
15	chr15:40949200-40957400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:40950000-40958600	Weak transcription	HUVEC	blood vessel
17	chr15:40950000-40958800	Weak transcription	HepG2	liver
18	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:40950200-40964200	Weak transcription	Osteobl	bone
20	chr15:40951800-40957800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:40953000-40960200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:40953800-40957400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:40953800-40960000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:40954600-40959800	Weak transcription	NHEK	skin
25	chr15:40954800-40958200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:40954800-40958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:40954800-40959600	Weak transcription	Liver	Liver
28	chr15:40954800-40960000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:40955000-40957600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:40955000-40958600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:40955200-40957600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:40955200-40958000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:40955200-40958200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:40955200-40958200	Weak transcription	Thymus	Thymus
35	chr15:40955200-40959800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:40955200-40961000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:40955200-40964400	Weak transcription	GM12878-XiMat	blood
38	chr15:40955200-40976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:40955200-40983200	Weak transcription	Fetal Intestine Small	intestine
40	chr15:40955400-40960400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:40955600-40959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:40955800-40976000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:40956800-40960400	Weak transcription	Fetal Thymus	thymus
44	chr15:40956800-40963000	Weak transcription	Hela-S3	cervix
45	chr15:40956800-40966000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:40956800-40971200	Weak transcription	Dnd41	blood
47	chr15:40957200-40957600	Enhancers	K562	blood
48	chr15:40957200-40958000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:40957200-40960600	Weak transcription	Fetal Stomach	stomach

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