Variant report

Variant	rs13116684
Chromosome Location	chr4:48037926-48037927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10025104	0.80[GIH][hapmap]
rs1003873	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs13121957	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145218	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13151608	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1348023	0.83[GIH][hapmap]
rs1507922	0.87[GIH][hapmap]
rs1567217	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs167692	0.83[GIH][hapmap]
rs2053404	0.80[GIH][hapmap]
rs224799	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279965	0.84[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2289433	0.80[GIH][hapmap]
rs321622	0.87[ASW][hapmap]
rs321630	0.82[ASW][hapmap]
rs321631	0.82[ASW][hapmap]
rs321632	0.81[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321634	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321635	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35085584	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694872	0.80[GIH][hapmap]
rs4695303	0.80[GIH][hapmap]
rs4695306	0.80[GIH][hapmap]
rs4695325	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55670663	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414687	0.80[GIH][hapmap]
rs6447609	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812991	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6818556	0.80[GIH][hapmap]
rs6841271	0.83[GIH][hapmap]
rs7674929	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9291317	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv967990	chr4:48037803-48041600	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13116684	TEC	cis	cerebellum	SCAN
rs13116684	NFXL1	cis	multi-tissue	Pritchard
rs13116684	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
3	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
4	chr4:48024600-48043600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48028200-48040800	Weak transcription	Gastric	stomach
7	chr4:48028200-48042600	Weak transcription	Placenta	Placenta
8	chr4:48031600-48041800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:48032800-48045000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:48033000-48045000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:48034000-48038600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
13	chr4:48034400-48039400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:48034800-48039200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:48034800-48041600	Strong transcription	HMEC	breast
16	chr4:48035000-48038000	Strong transcription	NHEK	skin
17	chr4:48035000-48039000	Weak transcription	Hela-S3	cervix
18	chr4:48035200-48038200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:48035800-48040200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:48036000-48038400	Weak transcription	Fetal Heart	heart
21	chr4:48036000-48040400	Enhancers	Primary B cells from peripheral blood	blood
22	chr4:48036200-48040000	Weak transcription	HepG2	liver
23	chr4:48036200-48041000	Enhancers	Primary B cells from cord blood	blood
24	chr4:48036400-48038000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:48036400-48038400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:48036400-48046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:48036600-48038200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr4:48036600-48040400	Weak transcription	Fetal Intestine Small	intestine
29	chr4:48036800-48038000	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr4:48036800-48038200	Strong transcription	Liver	Liver
31	chr4:48036800-48038400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr4:48037000-48039000	Strong transcription	Fetal Intestine Large	intestine
33	chr4:48037000-48039800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:48037400-48038000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:48037600-48038000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:48037600-48038200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:48037800-48038000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
38	chr4:48037800-48038400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr4:48037800-48038600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:48037800-48039000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:48037800-48039600	Enhancers	Primary T helper cells PMA-I stimulated	--

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