Variant report

Variant	rs2036565
Chromosome Location	chr5:118532871-118532872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10900728	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11241482	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12188483	1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs12516300	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs12518168	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12657132	1.00[JPT][hapmap]
rs13189818	1.00[JPT][hapmap]
rs1394629	0.85[CEU][hapmap]
rs3822516	0.87[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3923326	0.87[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3992621	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286709	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4565243	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4639262	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60504316	0.96[ASN][1000 genomes]
rs6595176	0.85[ASN][1000 genomes]
rs6874227	0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs7727906	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[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
rs2036565	COL6A1	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118451200-118533400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:118483000-118541400	Weak transcription	NHEK	skin
3	chr5:118485800-118534000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:118485800-118572200	Weak transcription	Small Intestine	intestine
5	chr5:118486000-118534200	Weak transcription	Brain Angular Gyrus	brain
6	chr5:118486000-118588600	Weak transcription	Right Ventricle	heart
7	chr5:118486200-118534200	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:118489800-118591200	Weak transcription	Colonic Mucosa	Colon
9	chr5:118494600-118534600	Weak transcription	Psoas Muscle	Psoas
10	chr5:118497800-118534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:118497800-118535200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:118498000-118534400	Weak transcription	Lung	lung
13	chr5:118498000-118584200	Weak transcription	Spleen	Spleen
14	chr5:118499800-118534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:118501800-118533000	Weak transcription	Left Ventricle	heart
16	chr5:118501800-118533800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:118501800-118533800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:118503800-118585800	Weak transcription	NH-A	brain
19	chr5:118504800-118533400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:118505400-118554600	Weak transcription	HepG2	liver
21	chr5:118507000-118533400	Weak transcription	HSMMtube	muscle
22	chr5:118507800-118580200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr5:118510000-118533400	Weak transcription	Aorta	Aorta
24	chr5:118510800-118533800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:118514200-118534000	Weak transcription	Brain Germinal Matrix	brain
26	chr5:118514400-118533200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:118514400-118533400	Weak transcription	Brain Anterior Caudate	brain
28	chr5:118514400-118533400	Weak transcription	Gastric	stomach
29	chr5:118514400-118533400	Weak transcription	Thymus	Thymus
30	chr5:118514400-118589000	Weak transcription	Pancreas	Pancrea
31	chr5:118514400-118591400	Weak transcription	Esophagus	oesophagus
32	chr5:118514600-118554800	Weak transcription	NHDF-Ad	bronchial
33	chr5:118516000-118544000	Weak transcription	Hela-S3	cervix
34	chr5:118516200-118533200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:118516200-118533200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:118516200-118533400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:118516200-118533400	Weak transcription	Brain Substantia Nigra	brain
38	chr5:118516200-118538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:118516200-118554800	Weak transcription	Osteobl	bone
40	chr5:118516400-118533200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:118520000-118533000	Weak transcription	Fetal Stomach	stomach
42	chr5:118520800-118533000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:118521200-118571000	Weak transcription	HMEC	breast
44	chr5:118522200-118533400	Weak transcription	Fetal Intestine Small	intestine
45	chr5:118523400-118533200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:118524200-118533200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:118524200-118533600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:118524200-118570800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr5:118524400-118571000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr5:118524600-118535400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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