Variant report

Variant	rs11871369
Chromosome Location	chr17:16542216-16542217
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs4239135	0.91[AFR][1000 genomes]
rs4791675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791679	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6502515	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7212915	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226328	0.89[ASW][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.93[AFR][1000 genomes]
rs8065506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072900	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080698	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9889868	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902518	0.87[EUR][1000 genomes]
rs9903721	0.83[EUR][1000 genomes]
rs9904209	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907721	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9908721	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9911269	0.89[ASN][1000 genomes]
rs9911518	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9911677	0.92[AFR][1000 genomes]
rs9916706	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9916819	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	esv2758442	chr17:16527056-16817437	Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2758676	chr17:16527056-16817437	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv427991	chr17:16527056-16817437	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11871369	DRG2	cis	parietal	SCAN
rs11871369	LLGL1	cis	parietal	SCAN
rs11871369	RAI1	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16527800-16556000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:16528000-16556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr17:16530000-16555400	Weak transcription	Small Intestine	intestine
4	chr17:16531200-16556200	Weak transcription	Right Ventricle	heart
5	chr17:16531600-16543800	Weak transcription	Stomach Mucosa	stomach
6	chr17:16531800-16556000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:16532200-16556000	Weak transcription	NHLF	lung
8	chr17:16532400-16556600	Weak transcription	Lung	lung
9	chr17:16533400-16556000	Weak transcription	HUVEC	blood vessel
10	chr17:16533400-16556400	Weak transcription	Aorta	Aorta
11	chr17:16535000-16556000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:16535000-16556000	Weak transcription	Spleen	Spleen
13	chr17:16535600-16556000	Weak transcription	Pancreas	Pancrea
14	chr17:16535800-16555400	Weak transcription	NHEK	skin
15	chr17:16536400-16556000	Weak transcription	Esophagus	oesophagus
16	chr17:16536600-16556000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr17:16537000-16542800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:16537200-16550400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:16537200-16556000	Weak transcription	Fetal Stomach	stomach
20	chr17:16537400-16547000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr17:16537400-16547200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:16537400-16548200	Weak transcription	Colon Smooth Muscle	Colon
23	chr17:16537400-16555600	Weak transcription	Fetal Brain Female	brain
24	chr17:16537400-16556000	Weak transcription	HMEC	breast
25	chr17:16537600-16555400	Weak transcription	Fetal Brain Male	brain
26	chr17:16537800-16556000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:16537800-16556000	Weak transcription	Fetal Thymus	thymus
28	chr17:16538000-16548000	Weak transcription	Brain Angular Gyrus	brain
29	chr17:16538000-16550200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr17:16538000-16555400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:16538000-16555400	Weak transcription	Brain Anterior Caudate	brain
32	chr17:16538000-16555400	Weak transcription	Brain Substantia Nigra	brain
33	chr17:16538000-16555400	Weak transcription	Psoas Muscle	Psoas
34	chr17:16538000-16556000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:16538000-16556000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr17:16538000-16556000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr17:16538000-16556000	Weak transcription	Thymus	Thymus
38	chr17:16538000-16556000	Weak transcription	NH-A	brain
39	chr17:16538000-16556000	Weak transcription	Osteobl	bone
40	chr17:16538000-16556400	Weak transcription	Left Ventricle	heart
41	chr17:16538200-16542400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr17:16538200-16542600	Weak transcription	HepG2	liver
43	chr17:16538200-16543400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:16538200-16544200	Weak transcription	Fetal Intestine Large	intestine
45	chr17:16538200-16545400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr17:16538200-16546200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr17:16538200-16548000	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr17:16538200-16548200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr17:16538200-16548200	Weak transcription	Placenta	Placenta
50	chr17:16538200-16550400	Weak transcription	Fetal Muscle Leg	muscle

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