Variant report

Variant	rs2412668
Chromosome Location	chr4:56493453-56493454
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56492253..56496567-chr4:56500430..56503372,5	K562	blood:
2	chr4:56492997..56495090-chr4:56501850..56503549,2	K562	blood:
3	chr4:56479641..56481239-chr4:56491828..56493480,2	K562	blood:

Variant related genes	Relation type
ENSG00000109255	Chromatin interaction

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

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

rs_ID	r²[population]
rs11133406	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11722402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11722645	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11723011	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11727450	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727729	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11727831	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11728776	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11729111	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11734493	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11735358	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11735654	0.93[AMR][1000 genomes]
rs11735815	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12499085	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12500147	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12501006	0.84[EUR][1000 genomes]
rs12502173	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12503046	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12503479	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12506506	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12507525	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12508869	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12509559	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35256215	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55665531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55885309	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56096459	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56260406	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73236154	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236155	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236156	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73236157	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73236159	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73236160	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73236161	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73236162	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73236163	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236164	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73236166	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73236167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73236168	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73236171	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73236173	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73236174	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73236175	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73236178	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236179	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236181	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73236182	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73236183	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236184	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236185	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236186	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73236187	0.93[AMR][1000 genomes];0.88[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	esv2762435	chr4:56478362-56494039	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	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
7	esv3393088	chr4:56484073-56503988	Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3395811	chr4:56486113-56514675	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412668	NMU	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56485400-56498000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:56485400-56498400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:56489400-56493800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:56489400-56498000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:56489800-56498200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:56491600-56496200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:56492000-56496400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:56492200-56495800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:56492200-56498200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:56492200-56498200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:56492400-56496600	Strong transcription	K562	blood
12	chr4:56492600-56498400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:56493400-56500200	Weak transcription	H1 Cell Line	embryonic stem cell

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