Variant report

Variant	rs2924388
Chromosome Location	chr15:40828682-40828683
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40825965..40829345-chr15:40829678..40833688,6	K562	blood:
2	chr15:40825263..40828833-chr15:40829678..40833530,4	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1037445	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10400890	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10400901	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10467972	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs11070275	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11070277	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070282	0.82[EUR][1000 genomes]
rs11070285	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11070286	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11632061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632370	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639464	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11852670	0.82[EUR][1000 genomes]
rs11852694	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11852828	0.82[EUR][1000 genomes]
rs11854986	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11855334	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11855923	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11856438	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11856802	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11858113	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12591207	0.82[EUR][1000 genomes]
rs12594548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905162	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12912058	0.81[JPT][hapmap]
rs12914743	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12916042	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16970851	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1806961	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1811513	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1813898	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869301	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1869302	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1967368	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1993212	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2034651	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2034652	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2167795	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2278888	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs2412531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412532	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412541	0.80[JPT][hapmap]
rs2412544	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2444302	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2898996	0.82[EUR][1000 genomes]
rs2924386	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2924387	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2959536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2959545	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3092978	0.80[JPT][hapmap]
rs3092979	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs35047458	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3751652	0.82[EUR][1000 genomes]
rs3751653	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4080706	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4923875	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924472	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924478	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924479	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924480	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924481	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924488	0.81[JPT][hapmap]
rs588686	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs590046	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs603623	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs616937	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs618399	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs619711	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs620198	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6492947	0.92[CEU][hapmap]
rs6492951	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs654317	0.84[EUR][1000 genomes]
rs6582	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71471881	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7167417	0.80[JPT][hapmap]
rs7169621	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171260	0.80[JPT][hapmap]
rs7177192	0.81[JPT][hapmap]
rs7178756	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7181074	0.80[EUR][1000 genomes]
rs7183273	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7494968	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8026605	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8028999	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs8029384	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034326	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8035775	0.81[JPT][hapmap]
rs8036737	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8037804	0.81[JPT][hapmap]
rs8038407	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8040502	0.81[JPT][hapmap]
rs8041534	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8042729	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs896795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9652415	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs976401	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2924388	C15orf57	cis	Nerve Tibial	GTEx
rs2924388	C15orf57	cis	Esophagus Muscularis	GTEx
rs2924388	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2924388	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2924388	CCDC32	cis	lesional skin	skin_eQTL
rs2924388	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs2924388	CCDC32	cis	normal skin	skin_eQTL
rs2924388	C15orf57	cis	Heart Left Ventricle	GTEx
rs2924388	C15orf57	cis	Lymphoblastoid	GTEx
rs2924388	C15orf57	cis	Cerebellum	GTEx
rs2924388	C15orf57	cis	Esophagus Mucosa	GTEx
rs2924388	C15orf57	cis	Artery Tibial	GTEx
rs2924388	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs2924388	C15orf57	cis	Artery Aorta	GTEx
rs2924388	C15orf57	cis	Muscle Skeletal	GTEx
rs2924388	C15orf57	cis	lung	GTEx
rs2924388	CCDC32	cis	multi-tissue	Pritchard
rs2924388	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs2924388	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2924388	RP11-111A22.1	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40805200-40833000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:40812400-40828800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:40812400-40828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:40812400-40829000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:40812400-40829000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:40812400-40831000	Weak transcription	Thymus	Thymus
7	chr15:40812400-40837800	Weak transcription	Lung	lung
8	chr15:40812600-40831400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:40812600-40840600	Weak transcription	Hela-S3	cervix
10	chr15:40816800-40835000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:40816800-40845600	Weak transcription	Ovary	ovary
12	chr15:40819200-40831200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:40819400-40830200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:40819400-40831200	Weak transcription	Gastric	stomach
15	chr15:40819600-40845000	Weak transcription	Pancreas	Pancrea
16	chr15:40820800-40833800	Weak transcription	K562	blood
17	chr15:40821200-40828800	Weak transcription	Fetal Intestine Small	intestine
18	chr15:40821400-40836800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:40821400-40848000	Weak transcription	Brain Anterior Caudate	brain
20	chr15:40821800-40840400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:40822600-40831400	Weak transcription	Aorta	Aorta
23	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
24	chr15:40822800-40831200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr15:40823200-40839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:40823800-40841800	Weak transcription	Brain Substantia Nigra	brain
27	chr15:40824800-40842600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:40825000-40836200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:40825200-40830400	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:40825400-40830400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:40825600-40839400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:40825600-40840000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:40825800-40829000	Weak transcription	NHLF	lung
34	chr15:40825800-40839200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:40825800-40839600	Weak transcription	NHEK	skin
36	chr15:40826200-40831400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:40826600-40831200	Weak transcription	Adipose Nuclei	Adipose
38	chr15:40827000-40831400	Strong transcription	Primary B cells from cord blood	blood
39	chr15:40827200-40830000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr15:40827200-40830200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:40827200-40831200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr15:40827200-40831600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:40827200-40833000	Weak transcription	GM12878-XiMat	blood
44	chr15:40827400-40829000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:40827600-40842000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:40827800-40829400	Enhancers	Fetal Stomach	stomach
47	chr15:40827800-40835400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:40827800-40839200	Weak transcription	Fetal Thymus	thymus
49	chr15:40828000-40829200	Enhancers	Fetal Intestine Large	intestine
50	chr15:40828000-40829800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links