Variant report

Variant	rs17672493
Chromosome Location	chr7:16236184-16236185
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10264415	0.81[EUR][1000 genomes]
rs10487915	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1527208	0.87[EUR][1000 genomes]
rs1527209	0.86[EUR][1000 genomes]
rs1527219	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1527220	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1527221	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1528136	0.84[CEU][hapmap]
rs17286418	0.82[EUR][1000 genomes]
rs17287882	0.86[EUR][1000 genomes]
rs17358277	0.81[EUR][1000 genomes]
rs17359183	0.86[EUR][1000 genomes]
rs17359294	0.87[EUR][1000 genomes]
rs17458603	0.87[EUR][1000 genomes]
rs1918259	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1918260	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1918266	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1918267	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1949952	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1978253	0.90[EUR][1000 genomes]
rs2058269	0.81[EUR][1000 genomes]
rs2214626	0.80[EUR][1000 genomes]
rs35150436	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3857709	0.84[EUR][1000 genomes]
rs4621696	0.84[EUR][1000 genomes]
rs4721485	0.87[EUR][1000 genomes]
rs56024841	0.88[EUR][1000 genomes]
rs56161298	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56279207	0.80[EUR][1000 genomes]
rs61282805	0.83[EUR][1000 genomes]
rs62440374	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62440376	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62440394	0.88[EUR][1000 genomes]
rs62440406	0.88[EUR][1000 genomes]
rs62440407	0.80[EUR][1000 genomes]
rs62442360	0.87[EUR][1000 genomes]
rs62442361	0.81[EUR][1000 genomes]
rs6956986	0.88[EUR][1000 genomes]
rs6961874	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6963052	0.93[EUR][1000 genomes]
rs6974124	0.88[EUR][1000 genomes]
rs73056339	0.87[EUR][1000 genomes]
rs7778438	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7782485	0.80[EUR][1000 genomes]
rs987932	0.92[CEU][hapmap]

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	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv949555	chr7:16078412-16279290	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1035015	chr7:16144928-16273061	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1847175	chr7:16155335-16272661	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv948950	chr7:16168925-16395434	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv887738	chr7:16211553-16284139	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv887739	chr7:16216494-16284139	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv887740	chr7:16216494-16286261	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv887741	chr7:16216494-16300179	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1030704	chr7:16236162-16271197	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv2757214	chr7:16236162-16334228	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2759514	chr7:16236162-16527390	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17672493	SOSTDC1	cis	parietal	SCAN
rs17672493	ANKMY2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16234000-16236200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr7:16234000-16238400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:16234400-16238400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:16234400-16238600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:16234800-16244000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:16235200-16236600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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