Variant report

Variant	rs9462426
Chromosome Location	chr6:38246773-38246774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38245020..38247639-chr6:38249479..38252433,2	MCF-7	breast:
2	chr6:38244443..38246917-chr6:38250103..38251748,2	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12524219	0.85[JPT][hapmap]
rs12529300	0.85[JPT][hapmap]
rs9470850	1.00[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9462426	C6orf130	cis	cerebellum	SCAN
rs9462426	TDRG1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

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	chr6:38239600-38247400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:38239600-38247800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:38239800-38257600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:38240000-38257800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:38241400-38246800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:38241600-38247600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:38241600-38258200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:38241800-38246800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:38241800-38246800	Weak transcription	Brain Anterior Caudate	brain
33	chr6:38241800-38247000	Weak transcription	Brain Angular Gyrus	brain
34	chr6:38241800-38247200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:38241800-38247800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:38243400-38257200	Weak transcription	Liver	Liver
37	chr6:38245000-38253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:38245800-38252400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:38246000-38249000	Enhancers	Brain Substantia Nigra	brain
40	chr6:38246200-38249600	Enhancers	Brain Hippocampus Middle	brain
41	chr6:38246400-38249000	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:38246400-38252600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:38246600-38249200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr6:38246600-38252400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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