Variant report

Variant	rs11124689
Chromosome Location	chr2:39873839-39873840
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39865680..39867303-chr2:39872989..39874953,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-1	chr2:39873811-39873915	NONHSAT070241

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10177801	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208929	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11124688	0.81[AFR][1000 genomes]
rs12613210	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12712652	0.88[EUR][1000 genomes]
rs12989245	0.88[EUR][1000 genomes]
rs13384364	0.83[EUR][1000 genomes]
rs13405084	0.84[EUR][1000 genomes]
rs13409487	0.88[EUR][1000 genomes]
rs1548870	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1548871	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1861244	0.88[EUR][1000 genomes]
rs2041736	0.87[EUR][1000 genomes]
rs2058618	0.89[EUR][1000 genomes]
rs2215956	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2540200	0.90[EUR][1000 genomes]
rs2540215	0.85[EUR][1000 genomes]
rs2540247	0.81[EUR][1000 genomes]
rs2540248	0.84[EUR][1000 genomes]
rs2540249	0.84[EUR][1000 genomes]
rs2540250	0.82[EUR][1000 genomes]
rs2540251	0.84[EUR][1000 genomes]
rs2540252	0.85[EUR][1000 genomes]
rs2540255	0.86[EUR][1000 genomes]
rs2716682	0.81[EUR][1000 genomes]
rs2716683	0.81[EUR][1000 genomes]
rs2716684	0.81[EUR][1000 genomes]
rs2716686	0.86[EUR][1000 genomes]
rs2716687	0.85[EUR][1000 genomes]
rs2716688	0.86[EUR][1000 genomes]
rs2716690	0.87[EUR][1000 genomes]
rs2716691	0.87[EUR][1000 genomes]
rs2716692	0.87[EUR][1000 genomes]
rs2716693	0.87[EUR][1000 genomes]
rs2716694	0.81[EUR][1000 genomes]
rs2716719	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2716720	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2716732	0.88[EUR][1000 genomes]
rs2716737	0.89[EUR][1000 genomes]
rs2716738	0.90[EUR][1000 genomes]
rs35791480	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4670952	0.85[EUR][1000 genomes]
rs6736442	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748628	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917964	0.86[EUR][1000 genomes]
rs9309041	0.84[EUR][1000 genomes]
rs949812	0.88[EUR][1000 genomes]
rs949813	0.86[EUR][1000 genomes]
rs9679346	0.85[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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39863400-39874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:39867600-39875600	Weak transcription	Psoas Muscle	Psoas
3	chr2:39869800-39874200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:39870000-39874200	Weak transcription	Stomach Mucosa	stomach
5	chr2:39870000-39874400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:39870200-39874000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:39870200-39874200	Weak transcription	HSMMtube	muscle

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