Variant report

Variant	rs4884021
Chromosome Location	chr13:76397731-76397732
allele	A/G
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	TCF12	chr13:76397671-76398270	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11617789	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4884023	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4885352	0.89[ASW][hapmap];0.93[CEU][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7334674	0.80[YRI][hapmap]
rs7981546	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7982790	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9573664	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4884021	LMO7	cis	parietal	SCAN
rs4884021	LMO7	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76361600-76397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
3	chr13:76373000-76414600	Weak transcription	HMEC	breast
4	chr13:76376800-76415400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:76377600-76398600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr13:76377600-76415800	Weak transcription	Dnd41	blood
7	chr13:76377600-76416200	Weak transcription	A549	lung
8	chr13:76378200-76397800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr13:76378200-76415800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:76378400-76415600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:76380600-76397800	Weak transcription	Colonic Mucosa	Colon
12	chr13:76380600-76397800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr13:76380600-76398000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr13:76380600-76400400	Weak transcription	Esophagus	oesophagus
15	chr13:76380600-76405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr13:76380800-76397800	Weak transcription	Brain Anterior Caudate	brain
17	chr13:76387400-76402000	Weak transcription	HUVEC	blood vessel
18	chr13:76387400-76403400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr13:76387400-76404200	Strong transcription	HSMMtube	muscle
20	chr13:76387800-76400000	Weak transcription	Fetal Stomach	stomach
21	chr13:76387800-76400400	Weak transcription	Spleen	Spleen
22	chr13:76387800-76402200	Strong transcription	HSMM	muscle
23	chr13:76387800-76415800	Weak transcription	Brain Germinal Matrix	brain
24	chr13:76387800-76427200	Weak transcription	Ovary	ovary
25	chr13:76388000-76397800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr13:76388000-76415200	Weak transcription	Fetal Brain Female	brain
27	chr13:76388800-76415400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr13:76389400-76414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr13:76390000-76402800	Weak transcription	Stomach Mucosa	stomach
30	chr13:76390200-76397800	Weak transcription	Right Ventricle	heart
31	chr13:76390400-76403600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:76390400-76405600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr13:76390600-76397800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr13:76390600-76401000	Strong transcription	Osteobl	bone
35	chr13:76390800-76397800	Weak transcription	Fetal Thymus	thymus
36	chr13:76391000-76398600	Strong transcription	HepG2	liver
37	chr13:76391000-76405600	Strong transcription	Liver	Liver
38	chr13:76391200-76400600	Strong transcription	NHDF-Ad	bronchial
39	chr13:76391200-76401600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr13:76391200-76418600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr13:76391200-76431600	Strong transcription	Hela-S3	cervix
42	chr13:76391400-76401000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:76391400-76402600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:76391400-76402800	Strong transcription	NH-A	brain
45	chr13:76391600-76415200	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:76392400-76400000	Strong transcription	NHLF	lung
47	chr13:76392400-76401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:76392400-76403400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr13:76392400-76415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr13:76393000-76399600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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