Variant report

Variant	rs2025028
Chromosome Location	chr14:39688297-39688298
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39653322..39655691-chr14:39686877..39688589,2	MCF-7	breast:
2	chr14:39687884..39690002-chr14:39715235..39717332,2	MCF-7	breast:
3	chr14:39637993..39640586-chr14:39685668..39689365,3	MCF-7	breast:
4	chr14:39638915..39642050-chr14:39686230..39689308,3	MCF-7	breast:
5	chr14:39686963..39689820-chr14:39735016..39736647,2	K562	blood:
6	chr14:39687526..39690139-chr14:39695809..39697449,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258940	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000182400	Chromatin interaction
ENSG00000258941	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10137623	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10144445	0.86[ASN][1000 genomes]
rs11622951	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12433610	0.89[JPT][hapmap]
rs1980609	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1998193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025027	0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2164066	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2415537	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35305286	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902459	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs56167516	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6571912	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7141840	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7153074	0.85[JPT][hapmap]
rs7153523	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs8019246	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8019368	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9322996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9743804	0.82[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	nsv1246	chr14:39656597-39701520	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv977460	chr14:39684663-39690168	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39674000-39705400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:39686400-39688400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:39686400-39688600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr14:39686400-39688600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:39686400-39688600	Enhancers	Small Intestine	intestine
6	chr14:39686400-39688600	Enhancers	HMEC	breast
7	chr14:39686400-39688600	Enhancers	NHEK	skin
8	chr14:39686400-39688800	Enhancers	HUVEC	blood vessel
9	chr14:39686600-39688600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr14:39686600-39688600	Enhancers	Stomach Mucosa	stomach
11	chr14:39686800-39688400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr14:39686800-39688600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr14:39686800-39688600	Enhancers	Fetal Intestine Large	intestine
14	chr14:39687200-39688600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr14:39687400-39688600	Enhancers	Fetal Intestine Small	intestine
16	chr14:39687400-39688600	Flanking Active TSS	HepG2	liver
17	chr14:39687400-39688600	Enhancers	NH-A	brain
18	chr14:39687800-39688600	Enhancers	HSMM	muscle
19	chr14:39688200-39688600	Enhancers	Primary B cells from peripheral blood	blood
20	chr14:39688200-39688600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr14:39688200-39688600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr14:39688200-39688600	Flanking Active TSS	A549	lung
23	chr14:39688200-39688600	Enhancers	GM12878-XiMat	blood
24	chr14:39688200-39688600	Flanking Active TSS	Hela-S3	cervix

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