Variant report

Variant	rs3777483
Chromosome Location	chr6:131573433-131573434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484765	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203075	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1358962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1407532	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1407533	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1729551	0.84[ASN][1000 genomes]
rs1885640	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs2146827	0.82[ASN][1000 genomes]
rs3777478	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777494	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850238	0.82[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4327722	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4484548	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61056763	0.82[EUR][1000 genomes]
rs6569737	0.84[EUR][1000 genomes]
rs66827112	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922252	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6924196	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7744734	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754788	0.89[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7755640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7761587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768335	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9321277	0.82[ASN][1000 genomes]
rs9375806	0.83[ASN][1000 genomes]
rs9398980	0.95[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs9483237	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9483239	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483244	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9483245	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9492886	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9800571	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv830808	chr6:131521115-131735320	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv1835599	chr6:131554291-131590766	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv886666	chr6:131573433-131666295	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3777483	SNORD101	cis	parietal	SCAN
rs3777483	VNN1	cis	cerebellum	SCAN
rs3777483	TAAR9	cis	parietal	SCAN
rs3777483	AKAP7	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131563000-131580000	Weak transcription	Small Intestine	intestine
2	chr6:131566800-131576200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:131567200-131576400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:131571000-131573600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:131571000-131573600	Active TSS	Duodenum Mucosa	Duodenum
6	chr6:131571000-131573800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:131571000-131574000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:131571000-131574400	Active TSS	Brain Germinal Matrix	brain
9	chr6:131571000-131574400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr6:131571000-131574400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:131571000-131574400	Active TSS	Fetal Intestine Large	intestine
12	chr6:131571200-131573600	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr6:131571200-131573800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:131571200-131574000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:131571200-131574000	Active TSS	Brain Hippocampus Middle	brain
16	chr6:131571200-131574200	Active TSS	Brain Cingulate Gyrus	brain
17	chr6:131571200-131574200	Active TSS	Fetal Brain Female	brain
18	chr6:131571200-131574400	Active TSS	Brain Angular Gyrus	brain
19	chr6:131571200-131575200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:131571600-131573800	Enhancers	Colon Smooth Muscle	Colon
21	chr6:131571600-131574000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:131571800-131574200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:131571800-131574200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:131571800-131576600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:131571800-131576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:131571800-131580000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:131571800-131583000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr6:131571800-131583200	Weak transcription	Aorta	Aorta
29	chr6:131571800-131587200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:131571800-131591400	Weak transcription	Psoas Muscle	Psoas
31	chr6:131571800-131592600	Weak transcription	Fetal Thymus	thymus
32	chr6:131571800-131596800	Weak transcription	Lung	lung
33	chr6:131571800-131603000	Weak transcription	Esophagus	oesophagus
34	chr6:131571800-131614400	Weak transcription	Gastric	stomach
35	chr6:131572000-131573800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:131572000-131573800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr6:131572000-131574400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:131572200-131573800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr6:131572200-131576600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:131572200-131576600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:131572200-131613000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:131572400-131573600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:131572400-131573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:131572400-131573800	Enhancers	Fetal Lung	lung
45	chr6:131572400-131574200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr6:131572400-131575000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:131572400-131576200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:131572400-131576200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:131572600-131573600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:131572600-131573800	Enhancers	Dnd41	blood

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