Variant report

Variant	rs2694394
Chromosome Location	chr12:105949244-105949245
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	chr12:105946907..105949767-chr12:106531210..106533511,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf75-6	chr12:105946682-105953346	NONHSAT030458

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10735407	0.80[ASN][1000 genomes]
rs10861456	0.88[EUR][1000 genomes]
rs10861457	0.88[EUR][1000 genomes]
rs10861461	0.81[ASN][1000 genomes]
rs11112595	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112596	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1317555	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1526844	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1526846	0.84[ASN][1000 genomes]
rs1806811	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1997174	0.88[EUR][1000 genomes]
rs2049571	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049572	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2374514	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2374515	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2694388	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2694390	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2694395	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2694398	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2694399	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2694400	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2694401	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2694404	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2711732	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2711734	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711735	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2711736	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2711737	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2711739	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711741	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2888859	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4468444	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs876929	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs885131	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941105	0.95[EUR][1000 genomes];0.98[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	nsv899501	chr12:105819046-105950801	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv832507	chr12:105821685-106005186	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1039068	chr12:105935786-106211250	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105938800-105964600	Weak transcription	Aorta	Aorta
2	chr12:105945400-105955000	Weak transcription	HSMMtube	muscle
3	chr12:105947200-105949400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:105947200-105950000	Enhancers	Hela-S3	cervix
5	chr12:105948200-105954000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:105948200-105955800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:105948400-105949400	Weak transcription	Right Ventricle	heart
8	chr12:105948400-105950000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:105948400-105955800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:105948600-105949800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:105949000-105949800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:105949000-105950200	Enhancers	A549	lung
13	chr12:105949200-105949400	Enhancers	Adipose Nuclei	Adipose
14	chr12:105949200-105949600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr12:105949200-105950000	Genic enhancers	HUVEC	blood vessel

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