Variant report

Variant	rs2102858
Chromosome Location	chr16:80334700-80334701
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:80334401..80335928-chr16:80343154..80345608,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1094134	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1094137	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11150257	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11150264	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11150265	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11150266	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11150267	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11150268	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11640342	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11645030	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11645305	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11646502	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12444960	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12448004	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12597946	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12924620	0.91[EUR][1000 genomes]
rs12935043	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1484033	0.85[EUR][1000 genomes]
rs1484034	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2139107	0.89[ASN][1000 genomes]
rs2170827	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2348640	0.89[EUR][1000 genomes]
rs2626634	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2626653	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4359452	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4360953	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4396547	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4448956	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7186257	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7187041	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7190266	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7193250	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7193273	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7196509	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7197047	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7201345	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7201635	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8044461	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs820810	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs820811	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs820812	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs875081	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs939000	0.85[EUR][1000 genomes]
rs9922405	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9923010	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055228	chr16:80207546-80378842	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1061068	chr16:80207546-80537052	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1063466	chr16:80227628-80360463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv573295	chr16:80251265-80341115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv949197	chr16:80284557-80456403	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1064628	chr16:80286004-80406177	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv542986	chr16:80286004-80406177	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv2762333	chr16:80307755-80509983	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv573296	chr16:80315263-80338877	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1056026	chr16:80317627-80471469	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv542987	chr16:80317627-80471469	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv906998	chr16:80320056-80371102	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2102858	CDH13	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80332200-80335000	Enhancers	NHDF-Ad	bronchial
2	chr16:80332200-80335400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr16:80332200-80335600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr16:80332200-80335800	Enhancers	HSMM	muscle
5	chr16:80332200-80336000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr16:80332400-80335200	Enhancers	Osteobl	bone
7	chr16:80332600-80335000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:80332600-80335600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:80332600-80335800	Enhancers	A549	lung
10	chr16:80332800-80334800	Enhancers	Aorta	Aorta
11	chr16:80332800-80334800	Enhancers	HUVEC	blood vessel
12	chr16:80332800-80335200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:80332800-80336000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr16:80333000-80340200	Weak transcription	Fetal Kidney	kidney
15	chr16:80333400-80334800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr16:80333400-80334800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:80333400-80335200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:80333400-80335200	Enhancers	HMEC	breast
19	chr16:80333400-80335600	Enhancers	NH-A	brain
20	chr16:80333400-80340400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr16:80333800-80335000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr16:80334000-80335200	Enhancers	NHEK	skin
23	chr16:80334000-80335600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr16:80334200-80334800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr16:80334200-80335000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr16:80334200-80336000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:80334400-80335200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr16:80334400-80337600	Weak transcription	Fetal Stomach	stomach
29	chr16:80334600-80334800	Enhancers	Placenta	Placenta
30	chr16:80334600-80335000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr16:80334600-80335200	Enhancers	HSMMtube	muscle
32	chr16:80334600-80335600	Weak transcription	Pancreas	Pancrea
33	chr16:80334600-80335600	Weak transcription	NHLF	lung
34	chr16:80334600-80335800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr16:80334600-80337200	Weak transcription	Fetal Lung	lung
36	chr16:80334600-80337200	Weak transcription	Fetal Muscle Leg	muscle

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