Variant report

Variant	rs32260
Chromosome Location	chr5:99868839-99868840
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10036140	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10043668	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11241571	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13876	0.96[CEU][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs152231	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs154711	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs154712	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs184888	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs190326	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2162836	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2370521	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2370612	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs247933	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs247936	0.84[ASW][hapmap];0.96[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs247937	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs247939	0.92[ASW][hapmap];0.96[CEU][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs247944	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs258540	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs258541	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs258546	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs258547	0.85[AMR][1000 genomes]
rs26028	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs26030	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26031	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs26032	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs26033	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs26034	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs27458	0.84[ASW][hapmap];0.96[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs27626	0.96[CEU][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs27885	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs32236	0.88[CEU][hapmap]
rs32237	0.88[CEU][hapmap]
rs32261	0.84[ASW][hapmap];0.96[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3907112	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs461591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs466613	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs493373	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs522628	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs573843	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6870025	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6884084	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7711475	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9765107	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759359	chr5:99207674-99883371	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2757124	chr5:99424756-99883371	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv882461	chr5:99745767-99927338	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1025132	chr5:99745775-99896429	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1025890	chr5:99745775-99936186	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv882463	chr5:99784116-99898851	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv882464	chr5:99784116-99905367	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv882465	chr5:99784116-99927338	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1018395	chr5:99827242-100003207	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs32260	MLX	trans	parietal	SCAN
rs32260	FAM174A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99866600-99870000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:99866800-99870000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:99866800-99870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:99867200-99869600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:99867400-99870000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:99867400-99870600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:99868200-99869800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:99868200-99870400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:99868200-99870400	Weak transcription	NHEK	skin
10	chr5:99868800-99870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:99868800-99870600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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