Variant report

Variant	rs11543742
Chromosome Location	chr7:117834049-117834050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:117833281..117835799-chr7:117836785..117838521,2	MCF-7	breast:
2	chr7:117123377..117126210-chr7:117833079..117835993,3	K562	blood:
3	chr7:117794437..117796815-chr7:117833814..117836624,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10085904	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10226152	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227326	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10229589	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10241875	0.88[EUR][1000 genomes]
rs10252627	0.87[EUR][1000 genomes]
rs10267938	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10487390	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1054032	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061731	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953864	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1117254	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11486992	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11770353	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979012	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12112697	0.81[EUR][1000 genomes]
rs12537795	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12667103	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12673046	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13224733	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041527	0.81[EUR][1000 genomes]
rs2041528	0.80[EUR][1000 genomes]
rs2058416	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2058417	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2191920	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2402322	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2896242	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802012	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4141028	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41900	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41901	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41902	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41905	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41906	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41909	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41910	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41911	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41915	0.89[EUR][1000 genomes]
rs41916	0.89[EUR][1000 genomes]
rs41926	0.89[EUR][1000 genomes]
rs41933	0.88[EUR][1000 genomes]
rs41934	0.89[EUR][1000 genomes]
rs41935	0.89[EUR][1000 genomes]
rs41938	0.89[EUR][1000 genomes]
rs41939	0.89[EUR][1000 genomes]
rs41960	0.83[EUR][1000 genomes]
rs5002233	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6466650	0.84[EUR][1000 genomes]
rs6944524	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6946855	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6948096	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6956486	0.93[EUR][1000 genomes]
rs6964911	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6965144	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7779933	0.92[EUR][1000 genomes]
rs7796145	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796148	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797855	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799229	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7806490	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917761	0.91[EUR][1000 genomes]
rs9655829	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9656260	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs979652	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886333	0.81[EUR][1000 genomes]
rs989899	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][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
rs11543742	LSM8	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117825000-117842200	Weak transcription	Aorta	Aorta
2	chr7:117825600-117835000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:117825600-117835600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:117825600-117837200	Weak transcription	Left Ventricle	heart
5	chr7:117825800-117834600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:117825800-117836600	Weak transcription	Psoas Muscle	Psoas
7	chr7:117825800-117842600	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:117826000-117834200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:117826000-117834200	Weak transcription	Fetal Brain Male	brain
10	chr7:117826000-117835200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:117827400-117834400	Strong transcription	Fetal Thymus	thymus
12	chr7:117827600-117834400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:117828000-117835600	Weak transcription	NHEK	skin
14	chr7:117828200-117834200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:117828400-117834400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:117828400-117835800	Weak transcription	Brain Substantia Nigra	brain
17	chr7:117828400-117836000	Weak transcription	Fetal Kidney	kidney
18	chr7:117828800-117835400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:117828800-117838800	Weak transcription	Primary B cells from cord blood	blood
20	chr7:117829200-117835400	Weak transcription	Colonic Mucosa	Colon
21	chr7:117829400-117834200	Weak transcription	HUVEC	blood vessel
22	chr7:117829800-117835600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:117829800-117840800	Weak transcription	Primary T cells from cord blood	blood
24	chr7:117830200-117834200	Strong transcription	K562	blood
25	chr7:117830400-117834200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:117830400-117834200	Weak transcription	Placenta	Placenta
27	chr7:117830400-117835200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:117830400-117842400	Weak transcription	Fetal Lung	lung
29	chr7:117830600-117834600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:117830600-117834800	Weak transcription	NHLF	lung
31	chr7:117830600-117835600	Weak transcription	A549	lung
32	chr7:117830800-117834800	Weak transcription	Fetal Intestine Large	intestine
33	chr7:117831000-117834200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:117831000-117835000	Strong transcription	Dnd41	blood
35	chr7:117831000-117835400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:117831200-117835200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr7:117831200-117835600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:117831200-117836000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:117831200-117842400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr7:117831400-117834200	Strong transcription	Hela-S3	cervix
41	chr7:117831400-117839800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:117832000-117835400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:117832200-117835400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:117832200-117836400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:117832600-117834200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:117832600-117834400	Weak transcription	NHDF-Ad	bronchial
47	chr7:117832600-117834400	Weak transcription	Osteobl	bone
48	chr7:117832600-117835600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr7:117832600-117836200	Weak transcription	Adipose Nuclei	Adipose
50	chr7:117832600-117836400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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