Variant report

Variant	rs7201829
Chromosome Location	chr16:82923681-82923682
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	chr16:82919356..82921414-chr16:82923083..82925361,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11150502	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs11150515	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11150516	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11150517	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11150518	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11862361	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12716955	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12928678	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1559311	0.86[ASN][1000 genomes]
rs1559312	0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs192598	1.00[YRI][hapmap]
rs192599	0.92[YRI][hapmap]
rs1991024	0.83[YRI][hapmap]
rs1991025	0.83[YRI][hapmap]
rs2059230	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2113138	0.83[YRI][hapmap]
rs2113140	0.85[CHB][hapmap]
rs2194285	0.88[MKK][hapmap];1.00[YRI][hapmap]
rs2194287	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2216739	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2549141	0.83[YRI][hapmap]
rs2615128	0.83[YRI][hapmap]
rs286678	1.00[YRI][hapmap]
rs286680	1.00[YRI][hapmap]
rs286687	1.00[YRI][hapmap]
rs4485358	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4513093	0.85[CHB][hapmap]
rs4782736	0.86[MEX][hapmap];0.91[YRI][hapmap]
rs4783290	0.83[YRI][hapmap]
rs4783292	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4783293	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs4783294	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[ASN][1000 genomes]
rs4783296	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6565075	0.85[CHB][hapmap];0.91[YRI][hapmap]
rs7184056	0.85[CHB][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs7184177	0.84[CHD][hapmap]
rs7197619	0.84[CHD][hapmap]
rs7199677	0.84[CHD][hapmap]
rs7201088	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs7498269	0.85[CHB][hapmap];0.85[YRI][hapmap]
rs8051136	0.86[MEX][hapmap];1.00[YRI][hapmap]
rs8052008	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs8052174	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8053647	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs8055355	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8063966	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs918660	0.85[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs918661	0.85[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs929846	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs929847	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs929848	0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs9319576	1.00[YRI][hapmap]
rs9319577	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs9319578	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs961283	0.86[CHB][hapmap]
rs9921828	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs9921848	0.86[YRI][hapmap]
rs9922147	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9929316	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9931196	0.85[CHB][hapmap];0.90[YRI][hapmap]
rs9933586	1.00[YRI][hapmap]
rs9933935	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs9936039	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057341	chr16:82363800-83198907	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv542997	chr16:82363800-83198907	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1063617	chr16:82786803-83229529	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers 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
6	esv2830385	chr16:82841335-82950413	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv573382	chr16:82905546-82950502	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1064158	chr16:82919690-82935671	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7201829	CDH13	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82905800-82924800	Weak transcription	HSMM	muscle
2	chr16:82905800-82925200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr16:82910400-82932600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:82915800-82953000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:82918800-82933400	Weak transcription	NHEK	skin
6	chr16:82922200-82924400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr16:82922400-82924800	Weak transcription	Psoas Muscle	Psoas
8	chr16:82922400-82925000	Weak transcription	HSMMtube	muscle
9	chr16:82922400-82925200	Weak transcription	Right Ventricle	heart
10	chr16:82922400-82925800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr16:82922600-82925000	Weak transcription	Aorta	Aorta
12	chr16:82922600-82925000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr16:82922600-82925000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr16:82922600-82925200	Weak transcription	Right Atrium	heart
15	chr16:82922600-82925800	Weak transcription	NH-A	brain
16	chr16:82922600-82933200	Weak transcription	Fetal Muscle Leg	muscle
17	chr16:82922600-82933200	Weak transcription	Left Ventricle	heart
18	chr16:82922800-82924800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr16:82922800-82925600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr16:82922800-82925600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr16:82922800-82925600	Weak transcription	Osteobl	bone

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