Variant report

Variant	rs2915178
Chromosome Location	chr11:34878051-34878052
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	chr11:34868671..34870522-chr11:34876282..34878999,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ELF5-3	chr11:34876859-34878189	XLOC_009414
2	lnc-ELF5-3	chr11:34877836-34878189	NONHSAT018762

Extended variants
information (count: 107 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1036070	0.83[ASN][1000 genomes]
rs1117051	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1117445	0.83[ASN][1000 genomes]
rs1396880	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1396881	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1509662	0.80[ASN][1000 genomes]
rs1549789	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549791	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1553757	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1553758	0.82[ASN][1000 genomes]
rs1553759	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1553760	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1553761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1553762	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1571135	0.91[GIH][hapmap]
rs1828298	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1858166	0.82[ASN][1000 genomes]
rs1960524	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1977420	0.91[GIH][hapmap]
rs1991648	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2031686	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2033355	0.85[ASN][1000 genomes]
rs2033357	0.83[ASN][1000 genomes]
rs2033358	0.83[ASN][1000 genomes]
rs2033360	0.83[ASN][1000 genomes]
rs2116085	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2116090	0.83[ASN][1000 genomes]
rs2147341	0.80[ASN][1000 genomes]
rs2163374	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163375	0.88[ASN][1000 genomes]
rs2303959	0.91[GIH][hapmap]
rs2421743	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2915177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2915179	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2915180	0.82[ASN][1000 genomes]
rs2915193	0.91[GIH][hapmap]
rs2915198	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2915205	0.91[GIH][hapmap]
rs2915208	0.83[ASN][1000 genomes]
rs2915214	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2915217	0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2915218	0.83[ASN][1000 genomes]
rs2915225	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2915226	0.83[ASN][1000 genomes]
rs2915228	0.83[ASN][1000 genomes]
rs2915230	0.83[ASN][1000 genomes]
rs2915231	0.83[ASN][1000 genomes]
rs2915232	0.83[ASN][1000 genomes]
rs2915233	0.83[ASN][1000 genomes]
rs2915235	0.83[ASN][1000 genomes]
rs2915237	0.88[ASN][1000 genomes]
rs2915238	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941040	0.95[ASN][1000 genomes]
rs2941041	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941042	0.82[ASN][1000 genomes]
rs2941043	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2941044	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941050	0.83[ASN][1000 genomes]
rs2941052	0.83[ASN][1000 genomes]
rs2941054	0.94[ASN][1000 genomes]
rs2941055	0.82[ASN][1000 genomes]
rs2941056	0.97[ASN][1000 genomes]
rs2941057	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941058	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941059	0.89[ASN][1000 genomes]
rs2941060	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2941061	0.83[ASN][1000 genomes]
rs2956074	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2956076	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2956077	0.82[JPT][hapmap]
rs2956078	0.98[ASN][1000 genomes]
rs2956079	0.88[ASN][1000 genomes]
rs2956080	0.83[ASN][1000 genomes]
rs2956084	0.83[ASN][1000 genomes]
rs2956086	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2956095	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2956097	1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2956109	0.81[ASN][1000 genomes]
rs2956112	0.91[CHB][hapmap]
rs2956114	0.91[GIH][hapmap]
rs2956116	0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2956118	0.81[ASN][1000 genomes]
rs2956120	0.83[ASN][1000 genomes]
rs2956125	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2985150	0.82[JPT][hapmap]
rs2985382	0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2985390	0.91[GIH][hapmap]
rs2986403	0.82[JPT][hapmap]
rs2986406	0.82[JPT][hapmap]
rs2986408	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2986410	0.89[GIH][hapmap]
rs2986413	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2986415	0.81[ASN][1000 genomes]
rs2986417	0.81[ASN][1000 genomes]
rs2986421	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2986425	0.91[GIH][hapmap]
rs2986427	0.91[GIH][hapmap]
rs520658	0.82[JPT][hapmap]
rs724714	0.85[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs7932442	0.83[EUR][1000 genomes]
rs891550	0.83[ASN][1000 genomes]
rs919554	0.83[ASN][1000 genomes]
rs925289	0.83[ASN][1000 genomes]
rs984690	0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][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	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	esv275183	chr11:34877761-34881376	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2915178	APIP	cis	Heart Left Ventricle	GTEx
rs2915178	TRIM44	cis	cerebellum	SCAN
rs2915178	APIP	cis	Esophagus Muscularis	GTEx
rs2915178	PDHX	Cis_1M	lymphoblastoid	RTeQTL
rs2915178	PDHX	cis	cerebellum	SCAN
rs2915178	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs2915178	APIP	cis	lymphoblastoid	seeQTL
rs2915178	APIP	cis	Nerve Tibial	GTEx
rs2915178	PDHX	cis	parietal	SCAN
rs2915178	APIP	cis	Thyroid	GTEx
rs2915178	APIP	cis	Artery Aorta	GTEx
rs2915178	PDHX	cis	lymphoblastoid	seeQTL
rs2915178	APIP	cis	Artery Tibial	GTEx
rs2915178	APIP	cis	multi-tissue	Pritchard
rs2915178	LOC728766///PRDM15	trans	lymphoblastoid	RTeQTL
rs2915178	APIP	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34859000-34909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:34872200-34886600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:34876200-34878200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:34876200-34878200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr11:34876400-34878800	Weak transcription	Small Intestine	intestine
6	chr11:34876600-34896000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:34876800-34880400	Weak transcription	Esophagus	oesophagus
8	chr11:34877000-34880800	Weak transcription	HepG2	liver
9	chr11:34877400-34881000	Weak transcription	Left Ventricle	heart
10	chr11:34877400-34886400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:34877600-34880000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:34877600-34881600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:34877600-34906400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:34877800-34878200	Enhancers	Fetal Muscle Leg	muscle
15	chr11:34877800-34878200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr11:34877800-34878800	Weak transcription	Stomach Mucosa	stomach
17	chr11:34878000-34878200	Enhancers	Psoas Muscle	Psoas
18	chr11:34878000-34880800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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