Variant report

Variant	rs12441754
Chromosome Location	chr15:40952092-40952093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40950840..40952962-chr15:40970003..40972550,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152546	0.81[EUR][1000 genomes]
rs10518697	0.89[EUR][1000 genomes]
rs1058734	0.82[EUR][1000 genomes]
rs11070283	0.86[EUR][1000 genomes]
rs11630273	0.85[EUR][1000 genomes]
rs11633184	0.84[EUR][1000 genomes]
rs11637245	0.81[EUR][1000 genomes]
rs11637422	0.83[EUR][1000 genomes]
rs12324748	0.84[EUR][1000 genomes]
rs12385982	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12903817	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12907442	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12908316	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12913296	0.81[EUR][1000 genomes]
rs12913739	0.85[EUR][1000 genomes]
rs12915171	0.81[EUR][1000 genomes]
rs12915636	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17673703	0.81[EUR][1000 genomes]
rs17674454	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17747423	0.89[EUR][1000 genomes]
rs17747633	0.89[EUR][1000 genomes]
rs1814541	0.85[EUR][1000 genomes]
rs2412525	0.84[EUR][1000 genomes]
rs28634695	0.81[EUR][1000 genomes]
rs28669075	0.81[EUR][1000 genomes]
rs28866515	0.80[AMR][1000 genomes]
rs28891195	0.81[AMR][1000 genomes]
rs34739056	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34824658	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs35127391	0.88[EUR][1000 genomes]
rs35684277	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35842610	0.85[EUR][1000 genomes]
rs4923880	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924486	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62019876	0.84[EUR][1000 genomes]
rs62019879	0.85[EUR][1000 genomes]
rs71471880	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7165509	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7170288	0.83[EUR][1000 genomes]
rs7175747	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8029530	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8036891	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8037180	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8038122	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8042386	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9920642	0.82[EUR][1000 genomes]
rs9920676	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12441754	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12441754	C15orf57	cis	Artery Aorta	GTEx
rs12441754	C15orf57	cis	Esophagus Mucosa	GTEx
rs12441754	RP11-111A22.1	cis	lung	GTEx
rs12441754	C15orf57	cis	Artery Tibial	GTEx
rs12441754	C15orf57	cis	Muscle Skeletal	GTEx
rs12441754	LOC283745	cis	brain	BrainEAC
rs12441754	C15orf57	cis	lung	GTEx
rs12441754	C15orf57	cis	Stomach	GTEx
rs12441754	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12441754	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12441754	C15orf57	cis	Heart Left Ventricle	GTEx
rs12441754	C15orf57	cis	Nerve Tibial	GTEx
rs12441754	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs12441754	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs12441754	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12441754	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12441754	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12441754	C15orf57	cis	Esophagus Muscularis	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
5	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
8	chr15:40913800-40986000	Weak transcription	A549	lung
9	chr15:40914400-40960000	Weak transcription	NHLF	lung
10	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
12	chr15:40922800-40954200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:40922800-40956000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:40923000-40954400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:40924000-40956600	Weak transcription	Fetal Brain Female	brain
16	chr15:40925000-40956200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:40925400-40956000	Weak transcription	Brain Germinal Matrix	brain
18	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:40939800-40956800	Strong transcription	Dnd41	blood
21	chr15:40939800-40956800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:40941400-40957600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:40942000-40959000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:40942200-40955800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr15:40942600-40955800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:40943000-40952200	Weak transcription	Fetal Intestine Small	intestine
27	chr15:40943000-40952800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:40943000-40956000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:40943000-40956000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
31	chr15:40943800-40953800	Weak transcription	Placenta	Placenta
32	chr15:40944600-40955200	Strong transcription	Thymus	Thymus
33	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:40945200-40961400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr15:40945800-40952800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:40946000-40954400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:40946400-40952400	Weak transcription	K562	blood
38	chr15:40946600-40953000	Weak transcription	Hela-S3	cervix
39	chr15:40946600-40957600	Weak transcription	HSMM	muscle
40	chr15:40946600-40957600	Weak transcription	NH-A	brain
41	chr15:40946600-40959800	Weak transcription	Gastric	stomach
42	chr15:40946800-40952400	Weak transcription	Fetal Intestine Large	intestine
43	chr15:40947200-40954200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:40947600-40956400	Weak transcription	HMEC	breast
45	chr15:40947800-40953000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:40949200-40957400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:40949400-40953800	Strong transcription	Fetal Muscle Leg	muscle
48	chr15:40949400-40955200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:40949600-40952800	Weak transcription	Spleen	Spleen
50	chr15:40949600-40955200	Strong transcription	Fetal Stomach	stomach

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