Variant report

Variant	rs6545021
Chromosome Location	chr2:48343949-48343950
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	chr2:48341598..48344591-chr2:48542825..48544946,2	K562	blood:
2	chr2:48342619..48344591-chr2:48541998..48544325,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXN2-5	chr2:48340114-48344953	NONHSAT070614

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10196696	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10199698	0.85[JPT][hapmap]
rs10865228	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11125165	0.89[ASN][1000 genomes]
rs11125166	0.81[ASN][1000 genomes]
rs1483213	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1483221	0.82[AMR][1000 genomes]
rs2056138	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2128719	0.83[ASN][1000 genomes]
rs2136456	0.96[ASN][1000 genomes]
rs2220075	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2348717	1.00[ASN][1000 genomes]
rs2348718	0.96[ASN][1000 genomes]
rs2882003	0.89[ASN][1000 genomes]
rs4146603	0.89[ASN][1000 genomes]
rs4952901	0.81[AMR][1000 genomes]
rs4952905	0.96[ASN][1000 genomes]
rs4953548	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953549	1.00[ASN][1000 genomes]
rs4953552	0.89[ASN][1000 genomes]
rs4953553	0.89[ASN][1000 genomes]
rs4953555	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4953556	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953557	0.89[ASN][1000 genomes]
rs58178746	0.89[ASN][1000 genomes]
rs58525908	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6545018	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6545023	0.89[ASN][1000 genomes]
rs6712238	1.00[ASN][1000 genomes]
rs6717617	0.85[JPT][hapmap]
rs6718037	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720994	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6722407	1.00[ASN][1000 genomes]
rs6723952	1.00[ASN][1000 genomes]
rs6732149	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6749276	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7566525	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7570354	0.89[ASN][1000 genomes]
rs7584401	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7584493	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7589460	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605361	1.00[ASN][1000 genomes]
rs7605366	0.90[ASN][1000 genomes]
rs7609124	1.00[ASN][1000 genomes]
rs922902	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs922903	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963134	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9677729	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs973894	0.89[ASN][1000 genomes]
rs990063	0.89[ASN][1000 genomes]
rs990549	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1000455	chr2:48202161-48362638	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv581773	chr2:48277490-48443109	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6545021	EPCAM	cis	cerebellum	SCAN
rs6545021	C2orf34	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48339400-48345000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48339600-48344600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:48340800-48347800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:48341000-48344400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr2:48341000-48345800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:48341200-48346600	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:48342200-48348200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:48342200-48353000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:48342400-48347000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:48342400-48347400	Weak transcription	K562	blood
11	chr2:48342400-48347800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:48342600-48347200	Weak transcription	Hela-S3	cervix
13	chr2:48342600-48348000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:48343800-48344200	Enhancers	GM12878-XiMat	blood

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