Variant report

Variant	rs17071960
Chromosome Location	chr13:49164195-49164196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10076	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs10467381	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11840819	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11842402	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11842662	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13378245	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071695	1.00[CHD][hapmap]
rs17071917	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs174854	0.90[AMR][1000 genomes]
rs174858	1.00[CHD][hapmap]
rs198565	0.90[AMR][1000 genomes]
rs198566	0.82[AMR][1000 genomes]
rs198567	0.82[AMR][1000 genomes]
rs198572	0.82[AMR][1000 genomes]
rs198573	0.90[AMR][1000 genomes]
rs198581	0.85[AMR][1000 genomes]
rs198583	0.90[AMR][1000 genomes]
rs198587	0.90[AMR][1000 genomes]
rs2804088	0.82[MEX][hapmap]
rs2984828	0.90[AMR][1000 genomes]
rs3020646	1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs411862	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs4151590	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs428431	0.82[AMR][1000 genomes]
rs449268	1.00[CHD][hapmap]
rs7322110	0.95[AMR][1000 genomes]
rs7332631	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7338141	0.92[AFR][1000 genomes]
rs7984270	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316386	1.00[CHD][hapmap]
rs9316392	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs9316396	1.00[CHD][hapmap]
rs9316403	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316406	0.92[AFR][1000 genomes]
rs9332025	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9332036	0.95[AMR][1000 genomes]
rs9332050	0.90[AMR][1000 genomes]
rs9332053	0.83[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes]
rs9332066	0.85[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs9591167	0.95[AMR][1000 genomes]
rs9591170	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591171	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9591174	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591175	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595913	0.90[AMR][1000 genomes]
rs9595917	0.95[AMR][1000 genomes]
rs9595930	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595936	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17071960	DDX6	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49157600-49164800	Weak transcription	Gastric	stomach
2	chr13:49159800-49164200	Weak transcription	Small Intestine	intestine
3	chr13:49160000-49166000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr13:49160200-49166200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:49161000-49169600	Weak transcription	HSMM	muscle
6	chr13:49161200-49164200	Weak transcription	Fetal Heart	heart
7	chr13:49161200-49164200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr13:49161200-49164200	Weak transcription	HSMMtube	muscle
9	chr13:49161200-49165400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr13:49161200-49167400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:49161200-49167400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr13:49161400-49164200	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:49161400-49164800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr13:49161400-49164800	Weak transcription	Pancreas	Pancrea
15	chr13:49161400-49169600	Weak transcription	Right Atrium	heart
16	chr13:49161400-49176400	Weak transcription	Right Ventricle	heart
17	chr13:49161600-49164600	Weak transcription	Left Ventricle	heart
18	chr13:49161600-49164800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:49161600-49165000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:49163000-49164800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:49163000-49167000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:49163200-49166600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr13:49163400-49164600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:49163600-49164200	Enhancers	Duodenum Mucosa	Duodenum
25	chr13:49163600-49165600	Enhancers	GM12878-XiMat	blood
26	chr13:49163600-49167400	Enhancers	Fetal Intestine Large	intestine
27	chr13:49163800-49164800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr13:49163800-49168200	Enhancers	Fetal Intestine Small	intestine
29	chr13:49163800-49170800	Enhancers	Stomach Mucosa	stomach
30	chr13:49164000-49165400	Enhancers	Placenta	Placenta
31	chr13:49164000-49169800	Enhancers	HepG2	liver

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