Variant report

Variant	rs10038484
Chromosome Location	chr5:178540026-178540027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178355351..178357900-chr5:178539539..178541563,2	K562	blood:
2	chr5:178538154..178541379-chr5:178543841..178547566,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM6-4	chr5:178537854-178540736	NONHSAT105574

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10057660	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10063310	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10067183	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10068311	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10072631	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10479525	0.90[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1049532	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1562233	0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1562234	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2161170	0.82[EUR][1000 genomes]
rs34320394	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3822591	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4701032	0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4701035	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4701036	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4701037	0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs4701038	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4701040	0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4701041	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4701042	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4701043	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4701046	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4701048	0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4701050	0.82[EUR][1000 genomes]
rs62393088	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6864241	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6868661	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6877691	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs716782	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7727747	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7728180	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][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	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1026790	chr5:178511268-178687428	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv482352	chr5:178525060-178697496	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10038484	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178527200-178540200	Weak transcription	HSMMtube	muscle
2	chr5:178527800-178559800	Weak transcription	HSMM	muscle
3	chr5:178538000-178544000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:178538000-178544400	ZNF genes & repeats	Liver	Liver
5	chr5:178538000-178550000	Strong transcription	Osteobl	bone
6	chr5:178538000-178560400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:178538200-178564600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:178538400-178542800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:178538400-178544000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr5:178538600-178540400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:178538600-178542800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:178538600-178543600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:178539000-178541600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
14	chr5:178539000-178543000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:178539200-178540400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:178539200-178540600	Weak transcription	NHLF	lung
17	chr5:178539400-178544400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr5:178539400-178545600	ZNF genes & repeats	Fetal Stomach	stomach
19	chr5:178539600-178542400	ZNF genes & repeats	Spleen	Spleen
20	chr5:178539800-178542800	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr5:178540000-178541800	ZNF genes & repeats	Fetal Muscle Trunk	muscle

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