Variant report

Variant	rs6725543
Chromosome Location	chr2:98910858-98910859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:98910684-98911144	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr2:98910715-98911285	HUVEC	blood vessel:	n/a	n/a
3	MYC	chr2:98910835-98911072	HUVEC	blood vessel:	n/a	n/a
4	JUN	chr2:98910462-98911486	HUVEC	blood vessel:	n/a	chr2:98910737-98910747 chr2:98910628-98910638 chr2:98910628-98910638 chr2:98910625-98910636
5	POLR2A	chr2:98910819-98911084	HUVEC	blood vessel:	n/a	n/a
6	GATA2	chr2:98910753-98911285	HUVEC	blood vessel:	n/a	chr2:98911191-98911202

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98910828..98912979-chr2:98930336..98932005,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000216112	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10172087	0.82[EUR][1000 genomes]
rs10176056	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10181000	0.87[CHB][hapmap]
rs10190336	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10199476	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs10201994	1.00[ASN][1000 genomes]
rs10202618	0.98[ASN][1000 genomes]
rs10203437	0.98[ASN][1000 genomes]
rs11124096	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs11124107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11124121	0.87[ASN][1000 genomes]
rs11673807	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11679920	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11889349	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11891512	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11895654	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs11901562	0.92[ASN][1000 genomes]
rs12478763	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12478769	0.82[ASN][1000 genomes]
rs12622324	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12624294	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712256	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12993718	0.82[ASN][1000 genomes]
rs12999985	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13013876	0.82[ASN][1000 genomes]
rs13014142	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13033263	0.82[ASN][1000 genomes]
rs13394706	0.90[ASW][hapmap];0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13408372	0.85[CHB][hapmap]
rs13415414	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13428221	0.83[ASN][1000 genomes]
rs1451251	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1466944	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs1504679	0.98[ASN][1000 genomes]
rs17427684	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17428056	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17429208	0.87[CHB][hapmap]
rs17493655	1.00[ASN][1000 genomes]
rs17493788	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875880	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2102270	0.87[CHB][hapmap];0.85[MEX][hapmap]
rs2122756	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs2202387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2221416	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2292118	0.87[CHB][hapmap]
rs2292119	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3731659	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4374424	1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4389366	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4455212	1.00[CHB][hapmap]
rs4477970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4479470	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4494805	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4535095	0.81[ASN][1000 genomes]
rs4608580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4632400	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4851122	0.92[ASN][1000 genomes]
rs4851123	0.98[ASN][1000 genomes]
rs4851124	0.98[ASN][1000 genomes]
rs4851935	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4851951	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4851952	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851954	0.94[ASN][1000 genomes]
rs4851955	0.98[ASN][1000 genomes]
rs4851959	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4851960	0.91[ASN][1000 genomes]
rs62157914	1.00[ASN][1000 genomes]
rs6543419	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6543459	1.00[ASN][1000 genomes]
rs66464436	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6715989	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs6742930	0.98[ASN][1000 genomes]
rs6747344	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6747410	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs6750975	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6754222	0.81[CHB][hapmap]
rs72819909	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72933220	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572757	1.00[ASN][1000 genomes]
rs7574218	0.82[ASN][1000 genomes]
rs7578802	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7589018	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7598554	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7601049	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7606070	0.98[ASN][1000 genomes]
rs7606220	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs937726	0.98[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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6725543	ANKRD39	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98898800-98913200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:98905000-98915600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:98910200-98911200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:98910200-98913200	Enhancers	Stomach Mucosa	stomach
5	chr2:98910400-98911000	Enhancers	HUVEC	blood vessel
6	chr2:98910400-98911400	Enhancers	Liver	Liver
7	chr2:98910800-98911000	Enhancers	Brain Hippocampus Middle	brain
8	chr2:98910800-98911200	Enhancers	Brain Angular Gyrus	brain
9	chr2:98910800-98911200	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:98910800-98911200	Enhancers	Brain Substantia Nigra	brain
11	chr2:98910800-98911400	Bivalent Enhancer	HepG2	liver
12	chr2:98910800-98911600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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