Variant report

Variant	rs12508869
Chromosome Location	chr4:56528836-56528837
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56523921..56526378-chr4:56528208..56530318,2	K562	blood:
2	chr4:56527671..56530669-chr4:56531905..56533687,2	K562	blood:
3	chr4:56507649..56509909-chr4:56526051..56528840,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11133406	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11722402	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11722645	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11723011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11727450	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11727729	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11727831	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11728776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729111	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11734493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11735358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11735654	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs11735815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12499085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12500147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12501006	0.86[EUR][1000 genomes]
rs12502173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12503046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12503479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12506506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12507525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2412668	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35256215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55665531	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55885309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56096459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56260406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73236154	0.93[AMR][1000 genomes]
rs73236155	0.93[AMR][1000 genomes]
rs73236156	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236157	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236159	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236160	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236161	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236162	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236163	0.93[AMR][1000 genomes]
rs73236164	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73236166	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236167	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236168	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73236173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73236174	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236175	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73236179	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73236181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73236182	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73236183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879021	chr4:56482750-56648713	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1006944	chr4:56512574-56580169	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv32833	chr4:56527823-56535040	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12508869	NMU	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56515400-56541400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:56525400-56530400	Weak transcription	K562	blood
3	chr4:56526600-56530400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:56527200-56530600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:56527600-56533800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:56527800-56534800	Weak transcription	H9 Cell Line	embryonic stem cell

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