Variant report

Variant	rs4146603
Chromosome Location	chr2:48400015-48400016
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	chr2:48397209..48400158-chr2:48400412..48403741,3	K562	blood:
2	chr2:48398522..48400210-chr2:48663770..48666421,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11125165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125166	0.85[ASN][1000 genomes]
rs1396826	0.88[YRI][hapmap]
rs1473611	0.80[EUR][1000 genomes]
rs1483215	0.80[EUR][1000 genomes]
rs2128719	0.93[ASN][1000 genomes]
rs2136456	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2348717	0.89[ASN][1000 genomes]
rs2348718	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2882003	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952905	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4953548	0.89[ASN][1000 genomes]
rs4953549	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953552	1.00[ASN][1000 genomes]
rs4953553	1.00[ASN][1000 genomes]
rs4953555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953556	1.00[ASN][1000 genomes]
rs4953557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58178746	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58525908	1.00[ASN][1000 genomes]
rs6545011	0.87[CEU][hapmap]
rs6545021	0.89[ASN][1000 genomes]
rs6545023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545024	0.88[YRI][hapmap]
rs6712238	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6718037	0.89[ASN][1000 genomes]
rs6722407	0.89[ASN][1000 genomes]
rs6723952	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6751603	1.00[YRI][hapmap]
rs7570354	1.00[ASN][1000 genomes]
rs7589460	0.89[ASN][1000 genomes]
rs7605361	0.89[ASN][1000 genomes]
rs7609124	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs922902	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922903	0.89[ASN][1000 genomes]
rs9677729	1.00[ASN][1000 genomes]
rs973894	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990063	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990549	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
rs4146603	FOXN2	cis	cerebellum	SCAN
rs4146603	FOXN2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48397000-48401800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:48397000-48401800	Weak transcription	Adipose Nuclei	Adipose
3	chr2:48397200-48401800	Weak transcription	Liver	Liver
4	chr2:48398000-48400800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:48398000-48401800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:48398400-48400200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:48399000-48400200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:48399000-48401800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:48399800-48401200	Enhancers	NHEK	skin
10	chr2:48399800-48402800	Enhancers	HMEC	breast
11	chr2:48400000-48400200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr2:48400000-48401200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:48400000-48401200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:48400000-48403000	Enhancers	Primary monocytes fromperipheralblood	blood

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