Variant report

Variant	rs509971
Chromosome Location	chr6:11567466-11567467
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs11751931	0.85[EUR][1000 genomes]
rs16871371	0.85[EUR][1000 genomes]
rs17607537	0.85[EUR][1000 genomes]
rs17607558	0.85[EUR][1000 genomes]
rs17675742	0.85[EUR][1000 genomes]
rs17675772	0.85[EUR][1000 genomes]
rs2140109	0.85[EUR][1000 genomes]
rs2177158	0.85[EUR][1000 genomes]
rs2177159	0.84[EUR][1000 genomes]
rs34066851	0.85[EUR][1000 genomes]
rs34255222	0.85[EUR][1000 genomes]
rs34336996	0.85[EUR][1000 genomes]
rs34342746	0.85[EUR][1000 genomes]
rs34363244	0.85[EUR][1000 genomes]
rs34486680	0.85[EUR][1000 genomes]
rs34586980	0.85[EUR][1000 genomes]
rs34630993	0.85[EUR][1000 genomes]
rs34678413	0.85[EUR][1000 genomes]
rs34793558	0.85[EUR][1000 genomes]
rs34951511	0.84[EUR][1000 genomes]
rs35074878	0.85[EUR][1000 genomes]
rs35087778	0.85[EUR][1000 genomes]
rs35100959	0.85[EUR][1000 genomes]
rs35250180	0.85[EUR][1000 genomes]
rs35491413	0.85[EUR][1000 genomes]
rs35658210	0.85[EUR][1000 genomes]
rs35877256	0.84[EUR][1000 genomes]
rs35938392	0.85[EUR][1000 genomes]
rs36021289	0.85[EUR][1000 genomes]
rs36023953	0.85[EUR][1000 genomes]
rs36053861	0.85[EUR][1000 genomes]
rs36120363	0.85[EUR][1000 genomes]
rs3942485	0.85[EUR][1000 genomes]
rs4711303	0.94[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4713556	0.85[EUR][1000 genomes]
rs4713562	0.94[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs4713569	0.85[EUR][1000 genomes]
rs4713577	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs4713579	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs471560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs471752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs478147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs483637	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs490466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513870	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs519140	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524159	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs528679	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs538808	0.92[ASN][1000 genomes]
rs539160	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs552681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554671	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs555742	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs566237	0.80[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs571683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs573082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574254	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs581285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs586105	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs598907	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs605058	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs606402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs620729	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs62394918	0.84[EUR][1000 genomes]
rs62394920	0.85[EUR][1000 genomes]
rs62394921	0.85[EUR][1000 genomes]
rs62394922	0.85[EUR][1000 genomes]
rs62394925	0.85[EUR][1000 genomes]
rs628980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs637564	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6457608	0.85[EUR][1000 genomes]
rs661055	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs663283	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66502560	0.85[EUR][1000 genomes]
rs67452935	0.85[EUR][1000 genomes]
rs675565	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67807015	0.84[EUR][1000 genomes]
rs678862	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687163	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6904209	0.83[EUR][1000 genomes]
rs6907890	0.85[EUR][1000 genomes]
rs6907900	0.85[EUR][1000 genomes]
rs6907944	0.85[EUR][1000 genomes]
rs6923613	0.85[EUR][1000 genomes]
rs6923798	0.84[EUR][1000 genomes]
rs6936326	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7752671	0.83[EUR][1000 genomes]
rs821443	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9348893	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357151	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9366802	0.85[EUR][1000 genomes]
rs9368729	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380321	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394108	0.85[EUR][1000 genomes]
rs9394109	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1015234	chr6:11545582-11583516	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs509971	TMEM170B	cis	Adipose Subcutaneous	GTEx
rs509971	GCNT2	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11556400-11568000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:11556800-11571600	Weak transcription	Ovary	ovary
3	chr6:11557000-11575600	Weak transcription	Spleen	Spleen
4	chr6:11557200-11575400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:11557400-11573200	Weak transcription	Psoas Muscle	Psoas
6	chr6:11563400-11575600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:11564200-11569200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:11564200-11573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:11564600-11572800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:11565200-11568800	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:11565200-11569600	Weak transcription	Fetal Thymus	thymus
12	chr6:11565200-11575400	Weak transcription	Right Ventricle	heart
13	chr6:11565800-11567800	Strong transcription	Primary B cells from cord blood	blood
14	chr6:11565800-11567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:11565800-11567800	Strong transcription	Adipose Nuclei	Adipose
16	chr6:11565800-11568200	Strong transcription	Primary T cells from cord blood	blood
17	chr6:11565800-11568200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:11565800-11568600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:11565800-11568600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:11565800-11569800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:11565800-11575400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:11566000-11567600	Strong transcription	Primary hematopoietic stem cells	blood
23	chr6:11566000-11568000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:11566000-11568600	Strong transcription	Dnd41	blood
25	chr6:11566000-11569000	Weak transcription	GM12878-XiMat	blood
26	chr6:11566200-11567800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:11566200-11568200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:11566400-11567600	Strong transcription	Fetal Brain Female	brain
29	chr6:11566400-11567600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr6:11566400-11568000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr6:11566600-11567600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:11566600-11567600	Strong transcription	Aorta	Aorta
33	chr6:11566600-11567600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:11566600-11567600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr6:11566600-11567600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:11566600-11567800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:11566600-11567800	Strong transcription	HSMMtube	muscle
38	chr6:11566600-11568200	Genic enhancers	Primary monocytes fromperipheralblood	blood
39	chr6:11566600-11568200	Strong transcription	Fetal Muscle Leg	muscle
40	chr6:11566600-11568200	Strong transcription	Placenta	Placenta
41	chr6:11566800-11567600	Strong transcription	Brain Substantia Nigra	brain
42	chr6:11566800-11567600	Strong transcription	Fetal Stomach	stomach
43	chr6:11566800-11567600	Strong transcription	Gastric	stomach
44	chr6:11566800-11567600	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr6:11566800-11567800	Strong transcription	Brain Anterior Caudate	brain
46	chr6:11566800-11567800	Strong transcription	Brain Hippocampus Middle	brain
47	chr6:11566800-11567800	Strong transcription	Lung	lung
48	chr6:11566800-11567800	Strong transcription	HepG2	liver
49	chr6:11566800-11568000	Strong transcription	Liver	Liver
50	chr6:11566800-11568000	Strong transcription	Brain Angular Gyrus	brain

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