Variant report

Variant	rs45604739
Chromosome Location	chr7:117825681-117825682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:116897859..116900656-chr7:117824567..117826449,2	K562	blood:
2	chr7:117825039..117827152-chr7:120589846..120592123,2	MCF-7	breast:
3	chr7:117822159..117825807-chr7:117854196..117858736,4	K562	blood:
4	chr2:234775602..234777791-chr7:117824084..117825749,2	MCF-7	breast:
5	chr7:117824273..117825955-chr7:117864602..117866522,2	MCF-7	breast:
6	chr7:117825257..117827852-chr7:118309009..118311377,2	K562	blood:

Variant related genes	Relation type
ENSG00000071243	Chromatin interaction
ENSG00000224287	Chromatin interaction
ENSG00000106013	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1015782	0.86[EUR][1000 genomes]
rs10247768	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487392	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11487110	0.86[EUR][1000 genomes]
rs11542074	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974039	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11983651	0.91[EUR][1000 genomes]
rs12154684	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12670769	0.83[EUR][1000 genomes]
rs1544583	0.94[EUR][1000 genomes]
rs1544584	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17140984	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17141053	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041527	0.81[EUR][1000 genomes]
rs2058418	0.84[EUR][1000 genomes]
rs2215628	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286863	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28260	0.83[EUR][1000 genomes]
rs33924981	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34010516	0.94[EUR][1000 genomes]
rs34019303	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35218902	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35485182	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41903	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41904	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41912	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41921	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41923	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41924	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41925	0.83[EUR][1000 genomes]
rs41930	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41931	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41936	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41962	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41989	0.82[EUR][1000 genomes]
rs4730837	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5002232	0.84[EUR][1000 genomes]
rs57308869	0.85[ASN][1000 genomes]
rs61328879	0.82[EUR][1000 genomes]
rs62466471	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62466515	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62468297	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62469806	0.90[EUR][1000 genomes]
rs6466643	0.82[EUR][1000 genomes]
rs6466648	0.86[EUR][1000 genomes]
rs6942513	0.82[EUR][1000 genomes]
rs6972105	0.80[EUR][1000 genomes]
rs769435	0.82[EUR][1000 genomes]
rs7786233	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7801976	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9641593	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656259	0.86[EUR][1000 genomes]
rs992035	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs45604739	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117822600-117825800	Active TSS	Psoas Muscle	Psoas
2	chr7:117823000-117825800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:117823000-117825800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr7:117823000-117826000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr7:117823000-117826000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:117823200-117826000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:117823400-117825800	Active TSS	Rectal Smooth Muscle	rectum
8	chr7:117823400-117826000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:117823400-117826000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr7:117823400-117826000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr7:117823400-117826000	Active TSS	Fetal Brain Female	brain
12	chr7:117823400-117826800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:117823600-117826600	Active TSS	K562	blood
14	chr7:117824400-117825800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr7:117824600-117825800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:117824600-117826000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr7:117824800-117825800	Flanking Active TSS	Liver	Liver
18	chr7:117824800-117826000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr7:117824800-117826000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr7:117824800-117826000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:117824800-117826000	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr7:117824800-117829000	Weak transcription	Lung	lung
23	chr7:117824800-117829200	Weak transcription	Gastric	stomach
24	chr7:117824800-117832600	Weak transcription	Pancreas	Pancrea
25	chr7:117825000-117825800	Enhancers	Brain Cingulate Gyrus	brain
26	chr7:117825000-117826000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr7:117825000-117826000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr7:117825000-117826000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:117825000-117826000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr7:117825000-117826000	Enhancers	Fetal Brain Male	brain
31	chr7:117825000-117826000	Enhancers	Small Intestine	intestine
32	chr7:117825000-117826200	Enhancers	Primary B cells from peripheral blood	blood
33	chr7:117825000-117826200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr7:117825000-117826600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:117825000-117827000	Weak transcription	Placenta	Placenta
36	chr7:117825000-117827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr7:117825000-117830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr7:117825000-117834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
40	chr7:117825200-117825800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr7:117825200-117825800	Enhancers	Spleen	Spleen
42	chr7:117825200-117825800	Flanking Active TSS	HMEC	breast
43	chr7:117825200-117826000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr7:117825200-117826000	Enhancers	Primary hematopoietic stem cells	blood
45	chr7:117825200-117826000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:117825200-117826000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr7:117825200-117826000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr7:117825200-117826000	Enhancers	Right Atrium	heart
49	chr7:117825200-117826000	Enhancers	Stomach Mucosa	stomach
50	chr7:117825200-117826200	Enhancers	Cortex derived primary cultured neurospheres	brain

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