Variant report

Variant	rs72846046
Chromosome Location	chr6:36810654-36810655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:36810456-36810668	GM12891	blood:	n/a	chr6:36810560-36810569 chr6:36810554-36810567
2	SPI1	chr6:36810459-36810670	GM12878	blood:	n/a	chr6:36810560-36810569 chr6:36810554-36810567
3	SPI1	chr6:36810448-36810685	GM12891	blood:	n/a	chr6:36810560-36810569 chr6:36810554-36810567

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36808554..36811671-chr6:36814361..36817752,3	MCF-7	breast:
2	chr6:36807425..36809491-chr6:36809760..36812415,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE5-1	chr6:36810625-36810866	XLOC_005701

Variant related genes	Relation type
CPNE5	TF binding region
ENSG00000124772	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10456445	0.85[EUR][1000 genomes]
rs11964396	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12111266	0.94[EUR][1000 genomes]
rs12111291	0.94[EUR][1000 genomes]
rs12524018	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12524422	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12524649	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12525180	0.84[EUR][1000 genomes]
rs12525540	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12526699	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529199	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12529769	0.93[EUR][1000 genomes]
rs17374068	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17552561	0.84[EUR][1000 genomes]
rs1864753	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35694858	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41408445	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4348312	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4714013	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55681762	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55913388	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56240344	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56302344	0.94[EUR][1000 genomes]
rs66474948	0.94[EUR][1000 genomes]
rs66566790	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67273613	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68042914	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72846078	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73416282	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7745555	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36808200-36811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:36808600-36818800	Weak transcription	Dnd41	blood
3	chr6:36808800-36816000	Weak transcription	Spleen	Spleen
4	chr6:36808800-36816600	Weak transcription	Aorta	Aorta
5	chr6:36809000-36811000	Weak transcription	Esophagus	oesophagus
6	chr6:36809000-36812200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr6:36809000-36813800	Enhancers	Fetal Muscle Leg	muscle
8	chr6:36809000-36816600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:36809000-36818600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:36809000-36820200	Weak transcription	Thymus	Thymus
11	chr6:36809000-36823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:36809200-36810800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:36809200-36810800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr6:36809200-36811200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:36809200-36812000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:36809200-36812200	Weak transcription	Brain Germinal Matrix	brain
17	chr6:36809200-36812200	Active TSS	Right Atrium	heart
18	chr6:36809200-36812400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:36809200-36812400	Weak transcription	Brain Angular Gyrus	brain
20	chr6:36809200-36812600	Weak transcription	Brain Substantia Nigra	brain
21	chr6:36809200-36812600	Weak transcription	Fetal Brain Female	brain
22	chr6:36809200-36816000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:36809200-36817000	Weak transcription	Brain Anterior Caudate	brain
24	chr6:36809200-36818000	Weak transcription	HSMM	muscle
25	chr6:36809200-36819200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:36809400-36810800	Weak transcription	Fetal Heart	heart
27	chr6:36809400-36811000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:36809400-36812000	Weak transcription	HSMMtube	muscle
29	chr6:36809400-36812000	Weak transcription	K562	blood
30	chr6:36809400-36812400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:36809400-36812400	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:36809800-36810800	Weak transcription	Left Ventricle	heart
33	chr6:36809800-36810800	Weak transcription	Psoas Muscle	Psoas
34	chr6:36809800-36811000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:36809800-36818400	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:36810000-36811000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:36810000-36813000	Enhancers	Fetal Muscle Trunk	muscle
38	chr6:36810400-36812000	Active TSS	Right Ventricle	heart
39	chr6:36810600-36811000	Enhancers	Duodenum Mucosa	Duodenum

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