Variant report

Variant	rs10896958
Chromosome Location	chr11:59036693-59036694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MPEG1-1	chr11:59036349-59039081	ENSG00000214797

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1048444	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10792228	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10896953	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896956	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229896	0.88[EUR][1000 genomes]
rs11229898	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11229899	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12280107	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17153461	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1938593	0.89[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1938594	0.81[CHB][hapmap]
rs1945592	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1945593	0.88[EUR][1000 genomes]
rs2000875	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3847	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4938915	0.87[EUR][1000 genomes]
rs4939260	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4939263	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4939267	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5023474	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5023475	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61689139	0.86[EUR][1000 genomes]
rs6591510	0.87[EUR][1000 genomes]
rs6591515	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6591517	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7109866	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7111287	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7113607	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115130	0.82[GIH][hapmap]
rs7121247	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7129035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7129362	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7931234	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7938115	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3381199	chr11:59015574-59068938	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1046084	chr11:59034871-59314519	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10896958	CYBASC3	cis	parietal	SCAN
rs10896958	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs10896958	FTH1	cis	parietal	SCAN
rs10896958	MPEG1	Cis_1M	lymphoblastoid	RTeQTL
rs10896958	UBE2L6	cis	parietal	SCAN
rs10896958	MPEG1	cis	lymphoblastoid	seeQTL
rs10896958	TMX2	cis	cerebellum	SCAN
rs10896958	SNORD28	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59029800-59039000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr11:59029800-59040400	Enhancers	Primary B cells from cord blood	blood
3	chr11:59031400-59039000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr11:59031800-59036800	Enhancers	Placenta	Placenta
5	chr11:59032600-59039200	Weak transcription	Spleen	Spleen
6	chr11:59034200-59040400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:59034400-59036800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:59035000-59038800	Weak transcription	Liver	Liver
9	chr11:59035000-59040600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr11:59035400-59037000	Genic enhancers	Primary B cells from peripheral blood	blood
11	chr11:59035800-59039400	Weak transcription	Stomach Mucosa	stomach
12	chr11:59036000-59037200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:59036000-59037400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr11:59036000-59038200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:59036000-59038400	Weak transcription	HMEC	breast
16	chr11:59036000-59039000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:59036000-59039000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:59036200-59040600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:59036600-59039000	Weak transcription	GM12878-XiMat	blood

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