Variant report

Variant	rs11685341
Chromosome Location	chr2:100636757-100636758
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	chr2:100633994..100635890-chr2:100636752..100639350,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10209110	0.81[EUR][1000 genomes]
rs10211595	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1062143	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11123804	0.82[ASN][1000 genomes]
rs11123805	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1115910	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12995420	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12997584	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2576678	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2871326	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6542905	0.82[ASN][1000 genomes]
rs6714788	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6733895	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6754099	0.82[ASN][1000 genomes]
rs7558817	0.82[ASN][1000 genomes]
rs7582731	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7599083	0.81[ASN][1000 genomes]
rs7605430	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs961788	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11685341	MRPL30	cis	cerebellum	SCAN
rs11685341	DUSP2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100615600-100638400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100624800-100657800	Weak transcription	Brain Germinal Matrix	brain
3	chr2:100626600-100637800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:100626800-100637600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:100627000-100637800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:100627800-100637800	Strong transcription	Primary B cells from cord blood	blood
7	chr2:100629400-100649600	Weak transcription	Fetal Brain Female	brain
8	chr2:100631800-100637400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:100633400-100645800	Weak transcription	Gastric	stomach
10	chr2:100633600-100638800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:100633600-100639600	Weak transcription	Thymus	Thymus
12	chr2:100633600-100652400	Weak transcription	Ovary	ovary
13	chr2:100633600-100653000	Weak transcription	Fetal Lung	lung
14	chr2:100633600-100660600	Weak transcription	Lung	lung
15	chr2:100634000-100637600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:100634400-100638200	Weak transcription	Primary T cells from cord blood	blood
17	chr2:100634800-100637400	Enhancers	Fetal Brain Male	brain
18	chr2:100636000-100638200	Weak transcription	NH-A	brain
19	chr2:100636200-100638000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr2:100636600-100637000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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