Variant report

Variant	rs17789266
Chromosome Location	chr6:114126613-114126614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13193860	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201785	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204232	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13207760	0.84[AMR][1000 genomes]
rs13209808	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13220044	0.84[AMR][1000 genomes]
rs2695454	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34206951	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34736881	0.84[AMR][1000 genomes]
rs34753135	0.84[AMR][1000 genomes]
rs34832025	0.84[AMR][1000 genomes]
rs34950886	0.84[AMR][1000 genomes]
rs352081	0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs352082	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs352084	0.85[JPT][hapmap]
rs35409527	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35470926	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35542449	0.84[AMR][1000 genomes]
rs35902942	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36000791	0.84[AMR][1000 genomes]
rs62417365	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66794022	0.84[AMR][1000 genomes]
rs71541084	0.84[AMR][1000 genomes]
rs72960759	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7747961	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3363275	chr6:114101331-114302866	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17789266	COL10A1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114125000-114132600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:114125600-114132400	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:114126000-114127400	Flanking Active TSS	GM12878-XiMat	blood
4	chr6:114126200-114127000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:114126200-114127000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:114126200-114127000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr6:114126200-114127000	Enhancers	Osteobl	bone
8	chr6:114126200-114127800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr6:114126400-114126800	Enhancers	Colon Smooth Muscle	Colon
10	chr6:114126400-114126800	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr6:114126400-114126800	Enhancers	Stomach Smooth Muscle	stomach
12	chr6:114126400-114127000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:114126400-114127200	Enhancers	Fetal Stomach	stomach
14	chr6:114126400-114127400	Enhancers	Fetal Lung	lung
15	chr6:114126400-114127600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr6:114126600-114126800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr6:114126600-114126800	Enhancers	Fetal Muscle Leg	muscle
18	chr6:114126600-114126800	Enhancers	HepG2	liver
19	chr6:114126600-114126800	Enhancers	HSMM	muscle
20	chr6:114126600-114126800	Enhancers	NHDF-Ad	bronchial
21	chr6:114126600-114127000	Enhancers	Brain Anterior Caudate	brain
22	chr6:114126600-114127000	Enhancers	Pancreas	Pancrea
23	chr6:114126600-114127000	Enhancers	Small Intestine	intestine
24	chr6:114126600-114127400	Enhancers	Rectal Smooth Muscle	rectum
25	chr6:114126600-114127600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:114126600-114127600	Enhancers	Brain Hippocampus Middle	brain
27	chr6:114126600-114127800	Enhancers	Skeletal Muscle Female	skeletal muscle

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