Variant report

Variant	rs3950680
Chromosome Location	chr11:17138666-17138667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10832731	0.85[EUR][1000 genomes]
rs11024149	0.86[EUR][1000 genomes]
rs11024151	0.82[EUR][1000 genomes]
rs11608038	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1236311	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12420958	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12575466	0.84[ASN][1000 genomes]
rs12577388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12577418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12577525	0.86[EUR][1000 genomes]
rs12577815	0.86[EUR][1000 genomes]
rs17472942	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17473243	0.86[EUR][1000 genomes]
rs17560341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17561348	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17641418	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1987694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs214091	0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap]
rs214105	0.80[GIH][hapmap];1.00[LWK][hapmap]
rs214903	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs214932	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214933	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs214934	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs214938	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34724588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34941502	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476890	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492263	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs522619	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs569780	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs586785	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60173525	0.86[EUR][1000 genomes]
rs615424	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61879692	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61881877	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61881881	0.85[EUR][1000 genomes]
rs644419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs664382	0.94[EUR][1000 genomes]
rs665311	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs679201	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7108067	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7478986	0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS 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	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3950680	DARS	trans	cerebellum	SCAN
rs3950680	TSG101	cis	cerebellum	SCAN
rs3950680	SERGEF	cis	parietal	SCAN
rs3950680	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs3950680	PDE3B	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17100400-17157200	Weak transcription	Fetal Heart	heart
2	chr11:17101600-17145000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:17105400-17172800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:17106800-17156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:17107000-17167200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:17107800-17147200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:17108200-17141400	Strong transcription	Liver	Liver
8	chr11:17108200-17177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:17108600-17172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:17109200-17144600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:17109400-17148400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:17109600-17147000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:17109800-17158400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:17111600-17182000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:17111800-17157800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:17115800-17154400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr11:17116800-17149800	Weak transcription	A549	lung
18	chr11:17117800-17147000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:17117800-17151800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:17118200-17139400	Strong transcription	Placenta	Placenta
21	chr11:17118200-17141400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:17118400-17139200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr11:17118400-17146800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:17120400-17157800	Weak transcription	Stomach Mucosa	stomach
25	chr11:17120400-17181600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr11:17120600-17155800	Weak transcription	Esophagus	oesophagus
27	chr11:17120800-17156200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:17120800-17166200	Weak transcription	Pancreas	Pancrea
29	chr11:17120800-17171800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:17120800-17172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:17121000-17178000	Weak transcription	Psoas Muscle	Psoas
32	chr11:17122200-17141600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:17122600-17145000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:17123000-17140000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:17124000-17144200	Strong transcription	Adipose Nuclei	Adipose
36	chr11:17125400-17172200	Weak transcription	Fetal Brain Male	brain
37	chr11:17125800-17181400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:17126000-17150000	Weak transcription	K562	blood
39	chr11:17126800-17143600	Weak transcription	NHDF-Ad	bronchial
40	chr11:17126800-17149400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr11:17126800-17149800	Weak transcription	Brain Angular Gyrus	brain
42	chr11:17126800-17186400	Weak transcription	Colonic Mucosa	Colon
43	chr11:17127200-17149000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:17127400-17149400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:17128000-17142400	Weak transcription	Gastric	stomach
46	chr11:17129200-17139200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr11:17129800-17138800	Strong transcription	Primary B cells from cord blood	blood
48	chr11:17129800-17140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:17129800-17147000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr11:17129800-17158200	Strong transcription	Primary monocytes fromperipheralblood	blood

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