Variant report

Variant	rs4884023
Chromosome Location	chr13:76399147-76399148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11617789	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12323251	0.85[ASN][1000 genomes]
rs12429913	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17715327	0.90[CHB][hapmap]
rs2275589	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs3736859	0.90[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3783024	1.00[ASN][1000 genomes]
rs4884021	0.83[ASW][hapmap];0.86[CEU][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4885352	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885353	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs4885356	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs7981546	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982790	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573664	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573665	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9573667	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9593132	0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9600559	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4884023	LMO7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
2	chr13:76373000-76414600	Weak transcription	HMEC	breast
3	chr13:76376800-76415400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:76377600-76415800	Weak transcription	Dnd41	blood
5	chr13:76377600-76416200	Weak transcription	A549	lung
6	chr13:76378200-76415800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr13:76378400-76415600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr13:76380600-76400400	Weak transcription	Esophagus	oesophagus
9	chr13:76380600-76405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:76387400-76402000	Weak transcription	HUVEC	blood vessel
11	chr13:76387400-76403400	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr13:76387400-76404200	Strong transcription	HSMMtube	muscle
13	chr13:76387800-76400000	Weak transcription	Fetal Stomach	stomach
14	chr13:76387800-76400400	Weak transcription	Spleen	Spleen
15	chr13:76387800-76402200	Strong transcription	HSMM	muscle
16	chr13:76387800-76415800	Weak transcription	Brain Germinal Matrix	brain
17	chr13:76387800-76427200	Weak transcription	Ovary	ovary
18	chr13:76388000-76415200	Weak transcription	Fetal Brain Female	brain
19	chr13:76388800-76415400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:76389400-76414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:76390000-76402800	Weak transcription	Stomach Mucosa	stomach
22	chr13:76390400-76403600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:76390400-76405600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr13:76390600-76401000	Strong transcription	Osteobl	bone
25	chr13:76391000-76405600	Strong transcription	Liver	Liver
26	chr13:76391200-76400600	Strong transcription	NHDF-Ad	bronchial
27	chr13:76391200-76401600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr13:76391200-76418600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr13:76391200-76431600	Strong transcription	Hela-S3	cervix
30	chr13:76391400-76401000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:76391400-76402600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:76391400-76402800	Strong transcription	NH-A	brain
33	chr13:76391600-76415200	Weak transcription	Brain Hippocampus Middle	brain
34	chr13:76392400-76400000	Strong transcription	NHLF	lung
35	chr13:76392400-76401200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:76392400-76403400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr13:76392400-76415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr13:76393000-76399600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr13:76393000-76416000	Weak transcription	Brain Angular Gyrus	brain
40	chr13:76393200-76399200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr13:76393200-76399400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr13:76393200-76399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr13:76393200-76399800	Weak transcription	Lung	lung
44	chr13:76393200-76405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:76393200-76405600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr13:76393400-76399400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr13:76393400-76415800	Weak transcription	Psoas Muscle	Psoas
48	chr13:76393600-76399800	Weak transcription	Fetal Muscle Leg	muscle
49	chr13:76393600-76414400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:76393600-76416000	Weak transcription	Fetal Lung	lung

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