Variant report

Variant	rs1952790
Chromosome Location	chr14:38342676-38342677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:38339276..38342707-chr14:38343768..38347145,3	MCF-7	breast:
2	chr14:38338833..38341519-chr14:38342499..38345279,2	MCF-7	breast:
3	chr14:38062426..38066513-chr14:38338443..38346839,18	MCF-7	breast:
4	chr14:38178359..38181904-chr14:38339541..38344216,4	MCF-7	breast:
5	chr14:38060189..38065879-chr14:38339920..38349339,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139865	Chromatin interaction
ENSG00000129514	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10134624	0.82[CEU][hapmap]
rs10140719	0.81[CEU][hapmap]
rs10145136	0.82[CEU][hapmap]
rs10146385	0.82[CEU][hapmap]
rs10872905	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11156973	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs11156974	0.82[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1170022	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs1170025	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs1170028	0.82[CEU][hapmap]
rs1170029	0.82[CEU][hapmap]
rs11851837	0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs12147106	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12432452	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs12590816	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs12882516	0.82[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap]
rs12883466	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs17179919	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs17554993	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs1952787	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1952789	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1958692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1958693	0.82[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1958694	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1959676	0.82[CEU][hapmap]
rs2415421	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2415422	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34953992	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35272292	0.87[EUR][1000 genomes]
rs3809444	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs4143919	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs4898785	0.93[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs4901412	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4901421	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs6571829	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs71407745	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71407747	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7154853	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8005651	0.82[CEU][hapmap]
rs8014896	0.80[CEU][hapmap]
rs8015738	0.82[CEU][hapmap]
rs9322983	0.82[CEU][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs954881	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv1051120	chr14:38294270-38436127	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv542046	chr14:38294270-38436127	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv564386	chr14:38311855-38365605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1952790	C14orf19	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38332400-38343600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:38334800-38343800	Weak transcription	Esophagus	oesophagus
3	chr14:38335000-38343800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr14:38335000-38343800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr14:38335600-38343600	Weak transcription	Gastric	stomach
6	chr14:38336200-38343600	Weak transcription	Fetal Intestine Small	intestine
7	chr14:38339000-38343600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr14:38339200-38343800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:38339800-38343800	Weak transcription	HSMM	muscle
10	chr14:38340000-38343800	Weak transcription	NHEK	skin
11	chr14:38340200-38343600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:38340400-38343800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr14:38340400-38343800	Weak transcription	A549	lung
14	chr14:38340400-38344000	Weak transcription	Adipose Nuclei	Adipose
15	chr14:38340400-38344000	Weak transcription	Fetal Muscle Leg	muscle
16	chr14:38340600-38344000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr14:38341000-38343600	Weak transcription	Colon Smooth Muscle	Colon
18	chr14:38341400-38343800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr14:38341600-38343600	Weak transcription	Liver	Liver
20	chr14:38342600-38343400	Weak transcription	HepG2	liver

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