Variant report

Variant	rs9544004
Chromosome Location	chr13:76191884-76191885
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	SIN3AK20	chr13:76191409-76191887	MCF-7	breast:	n/a	n/a
2	POLR2A	chr13:76191523-76192063	K562	blood:	n/a	n/a
3	POLR2A	chr13:76191498-76192252	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76191703..76193489-chr13:76193582..76195230,2	MCF-7	breast:

Variant related genes	Relation type
LMO7	TF binding region
ENSG00000136153	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12427755	0.96[ASN][1000 genomes]
rs12427931	0.96[ASN][1000 genomes]
rs12428989	0.96[ASN][1000 genomes]
rs1535724	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2031236	0.96[ASN][1000 genomes]
rs2296146	0.92[ASN][1000 genomes]
rs2328959	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2328960	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2328963	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328964	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2876706	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3783028	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818355	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4611344	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4885318	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4885322	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4885323	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4885324	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs55777620	0.95[ASN][1000 genomes]
rs55927305	0.89[ASN][1000 genomes]
rs6562913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6562914	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6562915	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6562916	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6562918	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7139740	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7317250	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73223968	0.92[ASN][1000 genomes]
rs73223984	0.96[ASN][1000 genomes]
rs7324195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329512	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7339146	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7981698	0.96[ASN][1000 genomes]
rs7982517	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7986566	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7989568	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7996884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8192755	0.96[ASN][1000 genomes]
rs8192756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8192762	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8192763	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8192764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9318361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9530447	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9543972	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9543976	0.92[ASN][1000 genomes]
rs9543990	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9543992	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9565177	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9573591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573592	0.99[ASN][1000 genomes]
rs974373	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv900571	chr13:76123678-76207565	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv900577	chr13:76132484-76207565	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	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
rs9544004	RP11-173B14.5	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76125000-76192800	Weak transcription	Brain Substantia Nigra	brain
2	chr13:76125000-76209600	Weak transcription	Right Ventricle	heart
3	chr13:76144000-76192400	Weak transcription	NHLF	lung
4	chr13:76144200-76194400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:76148200-76192200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:76148200-76203000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:76148200-76209600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr13:76149800-76209600	Weak transcription	Lung	lung
9	chr13:76158400-76192200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:76158600-76195200	Weak transcription	NHEK	skin
11	chr13:76159000-76194600	Weak transcription	HUVEC	blood vessel
12	chr13:76159000-76209600	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:76159400-76201800	Weak transcription	Fetal Lung	lung
14	chr13:76164600-76192000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr13:76164600-76194600	Weak transcription	Aorta	Aorta
16	chr13:76164600-76209400	Weak transcription	Esophagus	oesophagus
17	chr13:76165200-76209200	Weak transcription	Fetal Muscle Leg	muscle
18	chr13:76166800-76202000	Weak transcription	Fetal Brain Female	brain
19	chr13:76170800-76209600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr13:76174600-76198200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:76174600-76201400	Weak transcription	Psoas Muscle	Psoas
22	chr13:76176800-76199400	Weak transcription	Placenta	Placenta
23	chr13:76177600-76209400	Weak transcription	Left Ventricle	heart
24	chr13:76177600-76209600	Weak transcription	Fetal Stomach	stomach
25	chr13:76180000-76209600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr13:76180600-76204000	Weak transcription	GM12878-XiMat	blood
27	chr13:76180800-76204600	Weak transcription	Dnd41	blood
28	chr13:76180800-76209200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr13:76180800-76209200	Weak transcription	Adipose Nuclei	Adipose
30	chr13:76180800-76209600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr13:76181000-76194600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr13:76181000-76209400	Weak transcription	Fetal Thymus	thymus
33	chr13:76181000-76209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr13:76181000-76209600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr13:76181200-76192200	Weak transcription	Thymus	Thymus
36	chr13:76181200-76194400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:76181200-76198200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:76181200-76209400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr13:76181200-76209600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:76181400-76199600	Weak transcription	Primary B cells from cord blood	blood
41	chr13:76181400-76199600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr13:76181600-76194600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:76181600-76207400	Weak transcription	HMEC	breast
44	chr13:76182200-76198200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr13:76182800-76194200	Weak transcription	NH-A	brain
46	chr13:76182800-76209400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr13:76183000-76194400	Weak transcription	Fetal Heart	heart
48	chr13:76187400-76198000	Weak transcription	Primary T cells from cord blood	blood
49	chr13:76188000-76193000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:76189600-76209400	Weak transcription	Brain Inferior Temporal Lobe	brain

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