Variant report

Variant	rs9576707
Chromosome Location	chr13:39604614-39604615
allele	G/T
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	POLR2A	chr13:39604298-39604755	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:39595128..39597127-chr13:39603332..39605869,2	K562	blood:
2	chr13:39598668..39601223-chr13:39602617..39605478,2	MCF-7	breast:
3	chr13:39594195..39597127-chr13:39600978..39605869,5	K562	blood:

Variant related genes	Relation type
PROSER1	TF binding region
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11147745	0.96[ASN][1000 genomes]
rs12428445	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12429324	0.96[ASN][1000 genomes]
rs12429338	0.96[ASN][1000 genomes]
rs12430450	0.96[ASN][1000 genomes]
rs12431316	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1326405	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058947	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs17058990	1.00[ASN][1000 genomes]
rs17059014	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094252	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094253	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094254	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2104518	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274384	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274385	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2296648	0.96[ASN][1000 genomes]
rs34316151	0.95[ASN][1000 genomes]
rs34327528	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35804724	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864330	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3751377	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3751378	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3751379	0.96[ASN][1000 genomes]
rs3812879	0.89[ASN][1000 genomes]
rs4142398	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55809136	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66496062	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs66908302	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67296293	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73169457	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7317852	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318688	1.00[ASN][1000 genomes]
rs7327748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747752	0.96[ASN][1000 genomes]
rs7987207	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994530	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7997052	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998475	0.95[ASN][1000 genomes]
rs8000929	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566385	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9566389	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9566391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566393	0.90[ASN][1000 genomes]
rs9566396	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9566397	0.82[ASN][1000 genomes]
rs9576669	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9576670	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576673	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576674	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576676	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576677	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576678	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576679	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576681	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576683	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576684	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576685	0.95[ASN][1000 genomes]
rs9576686	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9576688	0.95[ASN][1000 genomes]
rs9576690	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576691	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9576692	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9576693	0.93[ASN][1000 genomes]
rs9576695	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576696	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576697	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9576698	0.96[ASN][1000 genomes]
rs9576699	0.96[ASN][1000 genomes]
rs9576700	0.96[ASN][1000 genomes]
rs9576701	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576703	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576710	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576711	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576717	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9576707	C13orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr13:39583200-39606600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr13:39587800-39608200	Weak transcription	Fetal Brain Male	brain
5	chr13:39588400-39608800	Weak transcription	Stomach Mucosa	stomach
6	chr13:39588600-39608200	Weak transcription	Hela-S3	cervix
7	chr13:39588600-39610400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:39589200-39608400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:39589200-39609400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:39591200-39608400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:39592400-39606600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr13:39594200-39605600	Strong transcription	Dnd41	blood
13	chr13:39594600-39605400	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr13:39594800-39605400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr13:39594800-39606400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr13:39594800-39608400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:39595000-39606400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:39595000-39606400	Strong transcription	HSMM	muscle
19	chr13:39595000-39606600	Strong transcription	Fetal Thymus	thymus
20	chr13:39595400-39605200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr13:39598000-39607800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:39598000-39609600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr13:39598200-39605200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:39598200-39606200	Weak transcription	Psoas Muscle	Psoas
25	chr13:39598200-39608800	Weak transcription	Fetal Heart	heart
26	chr13:39598400-39608400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr13:39598400-39609600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr13:39599000-39608200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr13:39599000-39608400	Weak transcription	Small Intestine	intestine
30	chr13:39599800-39605600	Strong transcription	Placenta	Placenta
31	chr13:39599800-39607600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr13:39599800-39608200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr13:39599800-39608400	Weak transcription	Aorta	Aorta
34	chr13:39599800-39608400	Weak transcription	Esophagus	oesophagus
35	chr13:39599800-39608400	Weak transcription	Fetal Intestine Small	intestine
36	chr13:39599800-39608400	Weak transcription	Left Ventricle	heart
37	chr13:39599800-39608400	Weak transcription	Pancreas	Pancrea
38	chr13:39599800-39608400	Weak transcription	Thymus	Thymus
39	chr13:39599800-39608400	Weak transcription	Spleen	Spleen
40	chr13:39599800-39608400	Weak transcription	A549	lung
41	chr13:39599800-39608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr13:39599800-39609000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:39599800-39609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr13:39599800-39609400	Weak transcription	Fetal Stomach	stomach
45	chr13:39599800-39609400	Weak transcription	Gastric	stomach
46	chr13:39599800-39609400	Weak transcription	Right Ventricle	heart
47	chr13:39599800-39610400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:39599800-39610600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:39599800-39611200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr13:39600000-39608200	Weak transcription	K562	blood

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