Variant report

Variant	rs3799566
Chromosome Location	chr6:167039406-167039407
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167027136..167029744-chr6:167037956..167040696,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10946178	0.94[CEU][hapmap];0.83[MKK][hapmap];0.80[EUR][1000 genomes]
rs10946179	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12196315	0.86[EUR][1000 genomes]
rs12199983	0.94[CEU][hapmap]
rs12203904	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs12204787	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs3778367	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs3778369	0.81[ASW][hapmap];0.94[CEU][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.82[EUR][1000 genomes]
rs3778370	0.81[ASW][hapmap];0.94[CEU][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.82[EUR][1000 genomes]
rs3778371	0.82[EUR][1000 genomes]
rs3778372	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs3778373	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3778375	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs3799570	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs3799571	0.94[CEU][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs58727224	0.82[EUR][1000 genomes]
rs60145177	0.82[EUR][1000 genomes]
rs6456097	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6456098	1.00[CEU][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6927052	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6929319	0.83[AFR][1000 genomes]
rs72503823	0.82[EUR][1000 genomes]
rs873070	0.94[CEU][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs873071	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs874153	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs916389	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9356498	0.94[CEU][hapmap]
rs9366034	0.83[CEU][hapmap]
rs9366035	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9459701	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv432984	chr6:167018915-167181613	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023649	chr6:167026469-167060732	Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3411974	chr6:167039387-167042335	Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3799566	RNASET2	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167034800-167039800	Weak transcription	Spleen	Spleen
2	chr6:167036800-167039600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:167037200-167039600	Weak transcription	Aorta	Aorta
4	chr6:167037200-167039600	Weak transcription	Esophagus	oesophagus
5	chr6:167037200-167039600	Weak transcription	Gastric	stomach
6	chr6:167037200-167039600	Weak transcription	Small Intestine	intestine
7	chr6:167037200-167039800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:167037800-167040000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:167038000-167039600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:167038200-167041800	Active TSS	Right Ventricle	heart
11	chr6:167038400-167042200	Active TSS	Psoas Muscle	Psoas
12	chr6:167038600-167040000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:167038600-167041800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:167038600-167042000	Active TSS	Lung	lung
15	chr6:167038800-167039800	Flanking Active TSS	HMEC	breast
16	chr6:167038800-167039800	Flanking Active TSS	NHEK	skin
17	chr6:167038800-167040000	Flanking Active TSS	Osteobl	bone
18	chr6:167039000-167039600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr6:167039000-167039600	Enhancers	Liver	Liver
20	chr6:167039000-167039800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:167039000-167039800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr6:167039000-167039800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:167039000-167039800	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr6:167039000-167039800	Flanking Active TSS	HUVEC	blood vessel
25	chr6:167039000-167041200	Active TSS	Right Atrium	heart
26	chr6:167039000-167041800	Active TSS	Left Ventricle	heart
27	chr6:167039200-167039600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr6:167039200-167039600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:167039200-167039600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr6:167039200-167039600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:167039200-167039600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr6:167039200-167039600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
33	chr6:167039200-167039600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr6:167039200-167039600	Flanking Active TSS	NHLF	lung
35	chr6:167039200-167039800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:167039200-167039800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr6:167039200-167040000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:167039200-167040000	Flanking Active TSS	NH-A	brain
39	chr6:167039200-167040200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:167039200-167040400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:167039200-167040600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
42	chr6:167039200-167041600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:167039200-167041800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:167039200-167041800	Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:167039200-167041800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr6:167039200-167041800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr6:167039200-167041800	Active TSS	HSMMtube	muscle
48	chr6:167039400-167039600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:167039400-167039600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:167039400-167039600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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