Variant report

Variant	rs1931767
Chromosome Location	chr6:38247845-38247846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1475761	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs228181	0.96[CEU][hapmap]
rs228182	0.91[CEU][hapmap]
rs228184	0.87[CEU][hapmap]
rs228185	0.91[CEU][hapmap]
rs228187	0.91[CEU][hapmap]
rs4711529	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4714136	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4714140	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs4714144	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6905637	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs6922620	0.91[CEU][hapmap]
rs9349067	0.87[EUR][1000 genomes]
rs9380737	0.83[CEU][hapmap]
rs9462424	0.89[EUR][1000 genomes]
rs9462425	0.93[EUR][1000 genomes]
rs9470847	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9470848	1.00[CEU][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9470849	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9470850	0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9470851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470856	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1931767	SPTLC3	trans	lymphoblastoid	RTeQTL
rs1931767	TRERF1	cis	cerebellum	SCAN
rs1931767	FTSJD2	cis	parietal	SCAN
rs1931767	C6orf106	cis	parietal	SCAN
rs1931767	C6orf64	cis	cerebellum	SCAN
rs1931767	ZFAND3	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38208200-38255000	Weak transcription	Ovary	ovary
2	chr6:38223600-38256000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:38224400-38267600	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38224600-38255200	Weak transcription	Primary B cells from cord blood	blood
5	chr6:38224800-38256400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:38225000-38255800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38226400-38258000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr6:38226600-38256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:38226600-38257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:38230200-38253400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:38230800-38256000	Weak transcription	Right Atrium	heart
12	chr6:38230800-38257800	Weak transcription	Pancreas	Pancrea
13	chr6:38231000-38250800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:38238000-38250400	Weak transcription	HUVEC	blood vessel
15	chr6:38238200-38257000	Weak transcription	Aorta	Aorta
16	chr6:38238400-38248200	Weak transcription	Fetal Brain Male	brain
17	chr6:38238400-38250200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:38238400-38255000	Weak transcription	Lung	lung
19	chr6:38238400-38258200	Weak transcription	Left Ventricle	heart
20	chr6:38238600-38258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:38239400-38248400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:38239400-38257800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:38239400-38259200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:38239800-38257600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr6:38240000-38257800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:38241600-38258200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:38243400-38257200	Weak transcription	Liver	Liver
28	chr6:38245000-38253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:38245800-38252400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:38246000-38249000	Enhancers	Brain Substantia Nigra	brain
31	chr6:38246200-38249600	Enhancers	Brain Hippocampus Middle	brain
32	chr6:38246400-38249000	Enhancers	Brain Cingulate Gyrus	brain
33	chr6:38246400-38252600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:38246600-38249200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr6:38246600-38252400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:38246800-38249000	Enhancers	Brain Anterior Caudate	brain
37	chr6:38246800-38249600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:38246800-38252200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:38247000-38249000	Enhancers	Brain Angular Gyrus	brain
40	chr6:38247200-38250600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr6:38247200-38257800	Weak transcription	Fetal Kidney	kidney
42	chr6:38247400-38248600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr6:38247400-38249200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr6:38247400-38250600	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr6:38247400-38252400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:38247600-38249200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:38247600-38249200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:38247800-38248400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:38247800-38248400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr6:38247800-38248800	Enhancers	Fetal Heart	heart

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