Variant report

Variant	rs10900728
Chromosome Location	chr5:118533828-118533829
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11241482	0.84[ASN][1000 genomes]
rs12188483	0.84[ASN][1000 genomes]
rs12518168	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036565	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822516	0.83[AMR][1000 genomes]
rs3923326	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3992621	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286709	0.85[EUR][1000 genomes]
rs4565243	0.82[ASN][1000 genomes]
rs4639262	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60504316	0.96[ASN][1000 genomes]
rs6595176	0.85[ASN][1000 genomes]
rs6874227	0.90[ASN][1000 genomes]
rs7727906	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1019788	chr5:118488501-118607405	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv537882	chr5:118488501-118607405	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1034616	chr5:118506348-118600391	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv1031914	chr5:118516878-118589497	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10900728	COL6A1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118483000-118541400	Weak transcription	NHEK	skin
2	chr5:118485800-118534000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:118485800-118572200	Weak transcription	Small Intestine	intestine
4	chr5:118486000-118534200	Weak transcription	Brain Angular Gyrus	brain
5	chr5:118486000-118588600	Weak transcription	Right Ventricle	heart
6	chr5:118486200-118534200	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:118489800-118591200	Weak transcription	Colonic Mucosa	Colon
8	chr5:118494600-118534600	Weak transcription	Psoas Muscle	Psoas
9	chr5:118497800-118534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:118497800-118535200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:118498000-118534400	Weak transcription	Lung	lung
12	chr5:118498000-118584200	Weak transcription	Spleen	Spleen
13	chr5:118499800-118534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:118503800-118585800	Weak transcription	NH-A	brain
15	chr5:118505400-118554600	Weak transcription	HepG2	liver
16	chr5:118507800-118580200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:118514200-118534000	Weak transcription	Brain Germinal Matrix	brain
18	chr5:118514400-118589000	Weak transcription	Pancreas	Pancrea
19	chr5:118514400-118591400	Weak transcription	Esophagus	oesophagus
20	chr5:118514600-118554800	Weak transcription	NHDF-Ad	bronchial
21	chr5:118516000-118544000	Weak transcription	Hela-S3	cervix
22	chr5:118516200-118538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:118516200-118554800	Weak transcription	Osteobl	bone
24	chr5:118521200-118571000	Weak transcription	HMEC	breast
25	chr5:118524200-118570800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr5:118524400-118571000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:118524600-118535400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:118524600-118536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:118524600-118537400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:118524600-118561200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:118524600-118584200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:118524800-118535200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr5:118525000-118535800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:118525200-118535800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr5:118525400-118536000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr5:118525400-118541000	Strong transcription	Liver	Liver
37	chr5:118525600-118536200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:118526000-118536000	Strong transcription	Primary B cells from cord blood	blood
39	chr5:118526400-118534000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:118527200-118534000	Weak transcription	Fetal Brain Male	brain
41	chr5:118527600-118537400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:118527800-118549000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:118528600-118536000	Weak transcription	HUVEC	blood vessel
44	chr5:118529400-118536200	Strong transcription	Dnd41	blood
45	chr5:118529600-118534200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:118529800-118534400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:118529800-118534800	Strong transcription	GM12878-XiMat	blood
48	chr5:118530000-118535200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:118531400-118534400	Weak transcription	Fetal Heart	heart
50	chr5:118531600-118534200	Strong transcription	Adipose Nuclei	Adipose

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