Variant report

Variant	rs4924554
Chromosome Location	chr15:41867079-41867080
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	chr15:41836227..41837993-chr15:41866817..41868834,2	K562	blood:

Variant related genes	Relation type
ENSG00000103932	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10438299	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1077714	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12906912	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12915829	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2246444	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277536	0.86[ASN][1000 genomes]
rs2277537	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2289743	0.86[ASN][1000 genomes]
rs2482307	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28655000	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28657602	0.92[ASN][1000 genomes]
rs28792443	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28844285	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3784283	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924552	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924556	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493004	0.87[ASN][1000 genomes]
rs6493005	0.86[ASN][1000 genomes]
rs66906913	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68058196	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7166371	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7183231	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8025165	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3312266	chr15:41865911-41870215	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3312265	chr15:41866000-41870088	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3312267	chr15:41866014-41870086	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4924554	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
2	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:41852600-41877400	Weak transcription	HMEC	breast
4	chr15:41852800-41877400	Weak transcription	NHEK	skin
5	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
6	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
7	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
9	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:41859000-41869000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:41859600-41868000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:41860800-41871800	Strong transcription	Brain Germinal Matrix	brain
14	chr15:41861000-41877200	Weak transcription	HUVEC	blood vessel
15	chr15:41861200-41867400	Weak transcription	Left Ventricle	heart
16	chr15:41861200-41870000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:41861200-41870000	Weak transcription	HSMMtube	muscle
18	chr15:41861200-41871200	Weak transcription	Small Intestine	intestine
19	chr15:41861200-41877000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:41861400-41867400	Weak transcription	Right Ventricle	heart
21	chr15:41861400-41868000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:41861400-41870000	Strong transcription	Fetal Muscle Leg	muscle
23	chr15:41861400-41870400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:41861400-41870400	Strong transcription	Fetal Stomach	stomach
25	chr15:41861400-41870600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr15:41861400-41870600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:41861400-41870800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:41861400-41871000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:41861400-41871400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:41861400-41871400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:41861400-41873200	Weak transcription	K562	blood
32	chr15:41861600-41868000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:41861600-41868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:41861600-41871400	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr15:41861600-41871400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:41861800-41868400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:41861800-41870000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:41861800-41870200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:41861800-41870200	Strong transcription	Spleen	Spleen
40	chr15:41861800-41871000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:41861800-41871000	Strong transcription	Fetal Intestine Large	intestine
42	chr15:41862000-41868200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:41862000-41870400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:41862000-41870600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr15:41862000-41870800	Strong transcription	Fetal Intestine Small	intestine
46	chr15:41862000-41871200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:41862200-41867800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:41862200-41867800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:41862200-41870800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:41862400-41868200	Strong transcription	Dnd41	blood

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