Variant report

Variant	rs7982479
Chromosome Location	chr13:48613635-48613636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr13:48613465-48613782	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr13:48613532-48613782	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr13:48612982-48613707	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOS	chr13:48613586-48613691	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr13:48613567-48613721	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:
2	chr13:48612235..48613841-chr13:48623262..48624820,2	K562	blood:
3	chr13:48612252..48613991-chr13:48614134..48616270,2	MCF-7	breast:
4	chr13:48612381..48615273-chr13:48617254..48619078,2	MCF-7	breast:
5	chr13:48612019..48613651-chr13:48806032..48808331,2	MCF-7	breast:

No data

Variant related genes	Relation type
SUCLA2	TF binding region
ENSG00000136156	Chromatin interaction
ENSG00000227848	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11148102	0.90[CHB][hapmap]
rs11838539	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs11841517	0.90[CHB][hapmap]
rs11842654	0.90[CHB][hapmap]
rs12428098	0.88[CHB][hapmap]
rs12431130	0.92[ASN][1000 genomes]
rs12584738	0.90[CHB][hapmap]
rs12585232	0.90[CHB][hapmap]
rs1410116	0.90[CHB][hapmap]
rs17071168	0.82[EUR][1000 genomes]
rs1964891	0.84[EUR][1000 genomes]
rs1964892	0.84[EUR][1000 genomes]
rs2182219	0.84[EUR][1000 genomes]
rs2182375	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2182377	0.95[EUR][1000 genomes]
rs2296572	0.90[CHB][hapmap]
rs3742108	0.90[CHB][hapmap]
rs3782979	1.00[CHB][hapmap]
rs4942741	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58316588	0.97[ASN][1000 genomes]
rs7325115	0.84[EUR][1000 genomes]
rs7336631	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7987109	0.84[EUR][1000 genomes]
rs7988917	0.94[EUR][1000 genomes]
rs7997347	0.88[CEU][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8002322	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs840430	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9526440	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9534910	0.95[EUR][1000 genomes]
rs9534936	0.91[EUR][1000 genomes]
rs9567962	0.95[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7982479	MED4	cis	multi-tissue	Pritchard
rs7982479	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs7982479	MED4	cis	normal skin	skin_eQTL
rs7982479	MED4	cis	lesional skin	skin_eQTL
rs7982479	MED4	cis	uninvolved skin	skin_eQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612400-48625000	Weak transcription	Spleen	Spleen
2	chr13:48612600-48614200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:48612600-48615400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:48612600-48616000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:48612600-48616000	Weak transcription	Left Ventricle	heart
6	chr13:48612600-48616000	Weak transcription	Lung	lung
7	chr13:48612600-48623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:48612600-48624200	Weak transcription	Gastric	stomach
9	chr13:48612600-48624800	Weak transcription	Ovary	ovary
10	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
13	chr13:48612800-48613800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr13:48612800-48613800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:48612800-48614200	Enhancers	Fetal Intestine Small	intestine
16	chr13:48612800-48614600	Weak transcription	Fetal Muscle Leg	muscle
17	chr13:48612800-48614600	Weak transcription	Fetal Stomach	stomach
18	chr13:48612800-48614800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr13:48612800-48615000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:48612800-48615400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:48612800-48616000	Weak transcription	Aorta	Aorta
22	chr13:48612800-48616000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr13:48612800-48620800	Weak transcription	Primary B cells from cord blood	blood
24	chr13:48612800-48622000	Weak transcription	Brain Germinal Matrix	brain
25	chr13:48612800-48622000	Weak transcription	Placenta	Placenta
26	chr13:48612800-48622200	Weak transcription	Fetal Brain Female	brain
27	chr13:48612800-48622400	Weak transcription	Brain Substantia Nigra	brain
28	chr13:48612800-48624600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr13:48612800-48624800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr13:48612800-48625000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr13:48612800-48628000	Weak transcription	Fetal Brain Male	brain
32	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
34	chr13:48613000-48614400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:48613000-48615000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:48613000-48615000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr13:48613000-48615200	Weak transcription	Adipose Nuclei	Adipose
38	chr13:48613000-48615200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr13:48613000-48615400	Weak transcription	Brain Angular Gyrus	brain
40	chr13:48613000-48615400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr13:48613000-48615400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr13:48613000-48617600	Weak transcription	HSMMtube	muscle
43	chr13:48613000-48621800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr13:48613000-48622200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr13:48613200-48613800	Enhancers	Duodenum Mucosa	Duodenum
48	chr13:48613200-48614000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr13:48613200-48614400	Enhancers	HepG2	liver
50	chr13:48613200-48614600	Weak transcription	Fetal Kidney	kidney

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