Variant report

Variant	rs29771
Chromosome Location	chr5:97976146-97976147
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13174024	0.80[AMR][1000 genomes]
rs13183889	0.81[CEU][hapmap]
rs1508791	0.81[EUR][1000 genomes]
rs152984	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs152985	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs152989	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs154206	0.83[ASN][1000 genomes]
rs162676	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs183628	1.00[CEU][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs251532	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2547958	0.81[EUR][1000 genomes]
rs2549200	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2591443	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2591445	0.80[AMR][1000 genomes]
rs2591447	0.84[CEU][hapmap]
rs2662250	0.80[AMR][1000 genomes]
rs27021	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs27022	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs27024	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27391	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs27575	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs27861	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28078	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs29768	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs29774	0.84[ASN][1000 genomes]
rs39579	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs466366	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs468562	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs469491	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs720859	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016611	chr5:97873846-98035559	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv537816	chr5:97873846-98035559	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1029509	chr5:97888644-98040172	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv882413	chr5:97918829-98022320	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29771	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97972000-97977600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:97972000-97977600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:97974400-97976600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:97974600-97976800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:97974600-97977200	Weak transcription	HSMMtube	muscle
6	chr5:97974600-97977400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:97974800-97979200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:97975000-97976200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:97975000-97979000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:97975200-97977000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:97975400-97976800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:97975400-97977000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:97975400-97977400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:97975400-97977400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:97975400-97977400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:97975400-97977600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:97975600-97977400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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