Variant report

Variant	rs11542074
Chromosome Location	chr7:117833054-117833055
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1015782	0.86[EUR][1000 genomes]
rs10247768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487392	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11487110	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11974039	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11983651	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12112697	0.84[CEU][hapmap]
rs12154684	0.92[CHB][hapmap];1.00[JPT][hapmap];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[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17140984	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17141053	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041527	0.81[EUR][1000 genomes]
rs2058418	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2215628	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286865	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs28260	0.83[EUR][1000 genomes]
rs33924981	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34010516	0.94[EUR][1000 genomes]
rs34019303	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35218902	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35485182	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41903	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41904	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41912	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41921	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41923	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41924	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41925	0.83[EUR][1000 genomes]
rs41930	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41931	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41936	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41962	0.82[EUR][1000 genomes]
rs41989	0.82[EUR][1000 genomes]
rs45604739	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730837	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[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	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62466515	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62468297	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	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs6972105	0.80[EUR][1000 genomes]
rs769435	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs7786233	0.92[CEU][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7801976	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9641593	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656259	0.86[EUR][1000 genomes]
rs992035	0.91[CEU][hapmap];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
rs11542074	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117825000-117834000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
3	chr7:117825200-117834000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:117825600-117834000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:117825600-117835000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:117825600-117835600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:117825600-117837200	Weak transcription	Left Ventricle	heart
8	chr7:117825800-117834000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:117825800-117834600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:117825800-117836600	Weak transcription	Psoas Muscle	Psoas
11	chr7:117825800-117842600	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:117826000-117833200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:117826000-117833600	Weak transcription	HepG2	liver
14	chr7:117826000-117834000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:117826000-117834200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:117826000-117834200	Weak transcription	Fetal Brain Male	brain
17	chr7:117826000-117835200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:117826400-117833200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:117826600-117834000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:117826800-117833400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:117827000-117833200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:117827000-117834000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:117827200-117833400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:117827400-117833400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr7:117827400-117833400	Strong transcription	Liver	Liver
26	chr7:117827400-117834000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr7:117827400-117834400	Strong transcription	Fetal Thymus	thymus
28	chr7:117827600-117833800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr7:117827600-117834400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:117827800-117833200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:117827800-117833600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:117828000-117833400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:117828000-117834000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:117828000-117835600	Weak transcription	NHEK	skin
35	chr7:117828200-117833200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr7:117828200-117833400	Strong transcription	GM12878-XiMat	blood
37	chr7:117828200-117834200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:117828400-117834400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:117828400-117835800	Weak transcription	Brain Substantia Nigra	brain
40	chr7:117828400-117836000	Weak transcription	Fetal Kidney	kidney
41	chr7:117828800-117835400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:117828800-117838800	Weak transcription	Primary B cells from cord blood	blood
43	chr7:117829200-117833200	Weak transcription	Fetal Brain Female	brain
44	chr7:117829200-117834000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:117829200-117835400	Weak transcription	Colonic Mucosa	Colon
46	chr7:117829400-117834000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:117829400-117834200	Weak transcription	HUVEC	blood vessel
48	chr7:117829600-117833200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr7:117829600-117834000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:117829600-117834000	Weak transcription	Ovary	ovary

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