Variant report

Variant	rs9576701
Chromosome Location	chr13:39593377-39593378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:39589682..39591724-chr13:39593267..39594841,2	K562	blood:
2	chr13:39593130..39595329-chr13:39596253..39597901,2	K562	blood:
3	chr13:39592251..39593878-chr13:39611776..39613438,2	MCF-7	breast:
4	chr13:39591603..39594467-chr13:39597947..39599911,2	K562	blood:
5	chr13:39589345..39592585-chr13:39593267..39595170,4	K562	blood:

Variant related genes	Relation type
ENSG00000188811	Chromatin interaction
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	0.96[ASN][1000 genomes]
rs12429324	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12429338	0.96[ASN][1000 genomes]
rs12430450	0.96[ASN][1000 genomes]
rs12431316	0.95[ASN][1000 genomes]
rs1326405	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058947	0.96[ASN][1000 genomes]
rs17058990	1.00[ASN][1000 genomes]
rs17059014	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094252	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094253	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2094254	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2104518	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274384	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274385	0.96[ASN][1000 genomes]
rs2296648	0.96[ASN][1000 genomes]
rs34316151	0.95[ASN][1000 genomes]
rs34327528	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35804724	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864330	0.95[ASN][1000 genomes]
rs3751377	0.96[ASN][1000 genomes]
rs3751378	0.96[ASN][1000 genomes]
rs3751379	0.96[ASN][1000 genomes]
rs3812879	0.89[ASN][1000 genomes]
rs4142398	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55809136	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66496062	0.95[ASN][1000 genomes]
rs66908302	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67296293	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73169457	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7317852	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318688	1.00[ASN][1000 genomes]
rs7327748	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747752	0.96[ASN][1000 genomes]
rs7987207	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994530	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7997052	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998475	0.95[ASN][1000 genomes]
rs8000929	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566385	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9566389	0.96[ASN][1000 genomes]
rs9566391	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566393	0.90[ASN][1000 genomes]
rs9566396	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9566397	0.82[ASN][1000 genomes]
rs9576669	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9576670	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576673	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576674	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576676	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576677	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576678	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576679	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576681	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576683	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576684	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576685	0.95[ASN][1000 genomes]
rs9576686	0.95[ASN][1000 genomes]
rs9576688	0.95[ASN][1000 genomes]
rs9576690	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576691	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9576692	0.95[ASN][1000 genomes]
rs9576693	0.93[ASN][1000 genomes]
rs9576695	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576696	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576697	0.96[ASN][1000 genomes]
rs9576698	0.96[ASN][1000 genomes]
rs9576699	0.96[ASN][1000 genomes]
rs9576700	0.96[ASN][1000 genomes]
rs9576703	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576705	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576707	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576710	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576711	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576717	0.91[AMR][1000 genomes];0.88[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
rs9576701	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	chr13:39581800-39597000	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr13:39582000-39596600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr13:39582000-39608200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:39582200-39593400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr13:39582200-39596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr13:39582200-39596800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr13:39582200-39597400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:39582400-39605400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr13:39582800-39593600	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr13:39583200-39606600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr13:39583600-39597200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr13:39584000-39597600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:39584600-39597600	Weak transcription	Fetal Heart	heart
14	chr13:39584600-39603600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr13:39586800-39596000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr13:39587800-39608200	Weak transcription	Fetal Brain Male	brain
17	chr13:39588400-39597000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:39588400-39608800	Weak transcription	Stomach Mucosa	stomach
19	chr13:39588600-39595000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:39588600-39597800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr13:39588600-39598800	Weak transcription	Brain Angular Gyrus	brain
22	chr13:39588600-39608200	Weak transcription	Hela-S3	cervix
23	chr13:39588600-39610400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:39588800-39595800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:39589200-39597800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:39589200-39598000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:39589200-39608400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr13:39589200-39609400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:39589400-39595000	Weak transcription	Brain Germinal Matrix	brain
30	chr13:39589400-39597600	Weak transcription	Spleen	Spleen
31	chr13:39589600-39594800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:39589600-39595000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr13:39589600-39595600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr13:39589600-39597200	Weak transcription	Small Intestine	intestine
35	chr13:39589800-39595000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr13:39589800-39595200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr13:39589800-39595600	Weak transcription	Brain Substantia Nigra	brain
38	chr13:39590000-39594800	Weak transcription	HepG2	liver
39	chr13:39590800-39595000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:39591000-39595000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr13:39591000-39595800	Weak transcription	Fetal Brain Female	brain
42	chr13:39591000-39596000	Weak transcription	Psoas Muscle	Psoas
43	chr13:39591200-39594800	Weak transcription	GM12878-XiMat	blood
44	chr13:39591200-39595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr13:39591200-39595000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr13:39591200-39595000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:39591200-39595000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:39591200-39595000	Weak transcription	K562	blood
49	chr13:39591200-39595200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr13:39591200-39599400	Weak transcription	Lung	lung

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