Variant report

Variant	rs72848004
Chromosome Location	chr6:36923521-36923522
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	chr6:36922482..36924199-chr6:36953592..36955477,2	K562	blood:
2	chr6:36923139..36925609-chr6:36953254..36955611,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17624006	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272194	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272198	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58012316	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406491	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406492	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406493	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406498	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406499	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406518	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs708005	0.89[EUR][1000 genomes]
rs708006	0.81[EUR][1000 genomes]
rs72846863	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72846873	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470445	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv519499	chr6:36915906-36924102	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv522653	chr6:36915906-36925774	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs72848004	PI16	cis	putamen	BrainEAC
rs72848004	PI16	cis	hippocampus	BrainEAC
rs72848004	PI16	cis	frontal cortex	BrainEAC
rs72848004	PI16	cis	inferior olivary nucleus	BrainEAC
rs72848004	PI16	cis	intralobular white matter	BrainEAC
rs72848004	PI16	cis	brain	BrainEAC
rs72848004	PI16	cis	thalamus	BrainEAC
rs72848004	PI16	cis	substantia nigra	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36917600-36931200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:36918000-36924000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:36918200-36927800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:36918200-36928400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:36921400-36924000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:36921400-36924200	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:36921400-36924400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:36921400-36924400	Enhancers	Thymus	Thymus
9	chr6:36921400-36925000	Enhancers	Fetal Thymus	thymus
10	chr6:36921600-36924400	Enhancers	Fetal Heart	heart
11	chr6:36921600-36925000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr6:36921800-36923600	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr6:36921800-36923600	Enhancers	Dnd41	blood
14	chr6:36921800-36923800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:36921800-36923800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr6:36921800-36926200	Enhancers	Stomach Mucosa	stomach
17	chr6:36921800-36931200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:36922000-36924000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:36922000-36924200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr6:36922000-36924200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr6:36922000-36931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:36922200-36924200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr6:36922200-36924600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:36922200-36929200	Weak transcription	Spleen	Spleen
25	chr6:36922400-36923800	Active TSS	Right Atrium	heart
26	chr6:36922400-36924200	Enhancers	Placenta	Placenta
27	chr6:36922600-36924000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:36922600-36924000	Enhancers	Esophagus	oesophagus
29	chr6:36922600-36924200	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:36922600-36924400	Active TSS	Stomach Smooth Muscle	stomach
31	chr6:36922800-36924000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr6:36922800-36924000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:36922800-36924200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:36922800-36924400	Enhancers	Hela-S3	cervix
35	chr6:36923000-36923800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr6:36923000-36923800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr6:36923000-36924200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:36923000-36924200	Enhancers	NHEK	skin
39	chr6:36923000-36924400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:36923200-36923600	Active TSS	Brain Anterior Caudate	brain
41	chr6:36923200-36923800	Enhancers	Brain Angular Gyrus	brain
42	chr6:36923200-36924000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:36923200-36924400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
44	chr6:36923200-36924400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:36923200-36924400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:36923200-36924600	Active TSS	Adipose Nuclei	Adipose
47	chr6:36923200-36927000	Weak transcription	Left Ventricle	heart
48	chr6:36923400-36923800	Enhancers	Duodenum Mucosa	Duodenum
49	chr6:36923400-36924200	Enhancers	Fetal Stomach	stomach
50	chr6:36923400-36930600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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