Variant report

Variant	rs7325115
Chromosome Location	chr13:48717024-48717025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1410116	0.82[MEX][hapmap]
rs1964891	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964892	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2182219	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182375	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2182377	0.83[AMR][1000 genomes]
rs4941618	0.90[MEX][hapmap]
rs4942741	0.86[EUR][1000 genomes]
rs7323702	1.00[MEX][hapmap]
rs7332363	1.00[MEX][hapmap]
rs7332994	1.00[MEX][hapmap]
rs7335797	0.90[MEX][hapmap]
rs7336631	0.86[EUR][1000 genomes]
rs7982479	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7987109	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	1.00[MEX][hapmap]
rs7996581	1.00[MEX][hapmap]
rs7997347	0.88[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes]
rs7999270	1.00[CHB][hapmap]
rs8002322	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes]
rs840430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9526440	0.86[EUR][1000 genomes]
rs9526455	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9534910	0.83[AMR][1000 genomes]
rs9534936	0.90[AMR][1000 genomes]
rs9534966	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9567962	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7325115	MED4	cis	uninvolved skin	skin_eQTL
rs7325115	MED4	cis	parietal	SCAN
rs7325115	MED4	cis	multi-tissue	Pritchard
rs7325115	MED4	cis	cerebellum	SCAN
rs7325115	MED4	cis	lesional skin	skin_eQTL
rs7325115	FAM194B	cis	cerebellum	SCAN
rs7325115	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs7325115	MED4	cis	normal skin	skin_eQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48701800-48725800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:48715600-48720600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr13:48716200-48717200	Enhancers	Primary B cells from cord blood	blood
4	chr13:48716200-48717400	Enhancers	Primary B cells from peripheral blood	blood
5	chr13:48716200-48720000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr13:48716400-48717200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr13:48716400-48718000	Weak transcription	Spleen	Spleen
8	chr13:48716400-48718800	Weak transcription	Lung	lung
9	chr13:48716600-48718000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr13:48716600-48726000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr13:48716800-48717200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr13:48716800-48718000	Weak transcription	Adipose Nuclei	Adipose
13	chr13:48716800-48718000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr13:48716800-48718200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:48717000-48718000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr13:48717000-48718000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr13:48717000-48718000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:48717000-48718000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr13:48717000-48718200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:48717000-48718200	Weak transcription	HUVEC	blood vessel
21	chr13:48717000-48718600	Weak transcription	HepG2	liver
22	chr13:48717000-48718800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr13:48717000-48718800	Weak transcription	GM12878-XiMat	blood

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