Variant report

Variant	rs2182375
Chromosome Location	chr13:48652590-48652591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48651976..48654376-chr13:48667767..48670618,2	K562	blood:

Variant related genes	Relation type
ENSG00000136146	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12427516	0.80[MKK][hapmap];0.82[ASN][1000 genomes]
rs12428055	0.82[ASN][1000 genomes]
rs12429099	0.82[ASN][1000 genomes]
rs12429348	0.80[MKK][hapmap];0.82[ASN][1000 genomes]
rs12429746	0.82[ASN][1000 genomes]
rs1410116	0.82[MEX][hapmap]
rs17071168	0.86[TSI][hapmap]
rs1964891	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1964892	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1968029	0.82[ASN][1000 genomes]
rs2094191	0.82[ASN][1000 genomes]
rs2182219	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2182377	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35710390	0.82[ASN][1000 genomes]
rs4941618	0.90[MEX][hapmap]
rs4942741	0.95[EUR][1000 genomes]
rs57957392	0.82[ASN][1000 genomes]
rs58634823	0.82[ASN][1000 genomes]
rs61585711	0.82[ASN][1000 genomes]
rs7323702	1.00[MEX][hapmap]
rs7325115	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7332363	1.00[MEX][hapmap]
rs7332994	1.00[MEX][hapmap]
rs7335797	0.90[MEX][hapmap]
rs7336631	0.95[EUR][1000 genomes]
rs7982479	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7987109	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7988917	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7990099	1.00[MEX][hapmap]
rs7991892	0.90[MEX][hapmap]
rs7996581	1.00[MEX][hapmap]
rs7997347	0.88[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs8002322	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs840430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526440	0.95[EUR][1000 genomes]
rs9526455	1.00[MEX][hapmap]
rs9534910	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9534936	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9534966	1.00[MEX][hapmap]
rs9567962	0.93[AMR][1000 genomes];0.98[EUR][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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2182375	MED4	cis	lesional skin	skin_eQTL
rs2182375	MED4	cis	multi-tissue	Pritchard
rs2182375	MED4	cis	parietal	SCAN
rs2182375	FAM194B	cis	cerebellum	SCAN
rs2182375	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs2182375	MED4	cis	cerebellum	SCAN
rs2182375	MED4	cis	uninvolved skin	skin_eQTL
rs2182375	MED4	cis	normal skin	skin_eQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48636600-48655400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr13:48640200-48661200	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr13:48640400-48655600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:48642600-48653800	Strong transcription	Brain Angular Gyrus	brain
5	chr13:48642800-48653800	Strong transcription	A549	lung
6	chr13:48644200-48657600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
7	chr13:48644200-48659800	Strong transcription	Stomach Smooth Muscle	stomach
8	chr13:48645200-48657600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr13:48645200-48661000	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr13:48645400-48654200	Strong transcription	Brain Hippocampus Middle	brain
11	chr13:48645400-48657600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr13:48645400-48657600	Strong transcription	NHLF	lung
13	chr13:48645600-48659800	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:48645600-48660400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr13:48645600-48660600	Strong transcription	Osteobl	bone
16	chr13:48645800-48660600	Strong transcription	HSMM	muscle
17	chr13:48645800-48661000	Strong transcription	HepG2	liver
18	chr13:48646000-48657400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr13:48646000-48660000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr13:48646000-48660000	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:48646200-48653000	Strong transcription	Psoas Muscle	Psoas
22	chr13:48646200-48655400	Strong transcription	Fetal Brain Male	brain
23	chr13:48646200-48656200	Strong transcription	HUVEC	blood vessel
24	chr13:48646200-48658200	Strong transcription	NHDF-Ad	bronchial
25	chr13:48646200-48661000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:48646400-48660400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr13:48646600-48657600	Strong transcription	Brain Substantia Nigra	brain
28	chr13:48646600-48658200	Strong transcription	Colon Smooth Muscle	Colon
29	chr13:48646600-48660400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:48646600-48660600	Strong transcription	Adipose Nuclei	Adipose
31	chr13:48646800-48653000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr13:48646800-48655200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr13:48646800-48658000	Strong transcription	NH-A	brain
34	chr13:48646800-48660000	Strong transcription	Fetal Intestine Large	intestine
35	chr13:48646800-48660400	Strong transcription	Placenta	Placenta
36	chr13:48647000-48660600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:48647000-48660800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:48647000-48662400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr13:48647200-48654600	Strong transcription	Fetal Kidney	kidney
40	chr13:48647200-48655400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:48647200-48660000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr13:48647200-48660600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:48647400-48660600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr13:48647400-48660600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr13:48647400-48660600	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr13:48647400-48663600	Weak transcription	Small Intestine	intestine
47	chr13:48647600-48660400	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr13:48647800-48656200	Strong transcription	HMEC	breast
49	chr13:48647800-48658400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr13:48648000-48658200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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