Variant report

Variant	rs4647713
Chromosome Location	chr11:47239270-47239271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47205689..47216568-chr11:47232414..47239487,27	MCF-7	breast:
2	chr11:47236414..47239398-chr11:47265054..47267561,5	K562	blood:
3	chr11:47238223..47239745-chr11:47245693..47248680,2	K562	blood:
4	chr11:47236760..47239573-chr11:47432455..47434658,2	K562	blood:
5	chr11:47237709..47239872-chr11:47292280..47293841,2	MCF-7	breast:
6	chr11:47205217..47215436-chr11:47233934..47241095,26	MCF-7	breast:
7	chr11:47238955..47241531-chr11:47289133..47291443,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256746	Chromatin interaction
ENSG00000243802	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000165912	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12573962	0.81[ASN][1000 genomes]
rs12574558	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12575296	0.81[ASN][1000 genomes]
rs12576461	0.81[ASN][1000 genomes]
rs12576690	0.81[ASN][1000 genomes]
rs12576751	0.81[ASN][1000 genomes]
rs12576831	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12576839	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12576935	0.84[ASN][1000 genomes]
rs12578030	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197500	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17197619	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17197710	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17790246	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17790306	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17790336	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17790342	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17790390	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17790420	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3736101	0.81[ASN][1000 genomes]
rs3816724	0.81[ASN][1000 genomes]
rs41301449	0.81[ASN][1000 genomes]
rs4572092	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4647720	0.80[ASN][1000 genomes]
rs4647759	0.81[ASN][1000 genomes]
rs55968738	0.87[ASN][1000 genomes]
rs57012996	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57964319	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59689332	0.87[ASN][1000 genomes]
rs60041842	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60088916	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60174717	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60201196	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60335739	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61142746	0.87[ASN][1000 genomes]
rs61896051	0.81[ASN][1000 genomes]
rs61896053	0.81[ASN][1000 genomes]
rs61896054	0.81[ASN][1000 genomes]
rs61896120	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896121	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896122	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896124	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896125	0.93[ASN][1000 genomes]
rs61896126	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61896131	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61896132	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61897776	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897777	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897782	0.90[ASN][1000 genomes]
rs61897784	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897786	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61897788	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897791	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61897843	0.92[AMR][1000 genomes]
rs61897851	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897852	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61897853	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61897854	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897855	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897856	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897858	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899284	0.87[ASN][1000 genomes]
rs61899285	0.87[ASN][1000 genomes]
rs61899293	0.87[ASN][1000 genomes]
rs61899294	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4647713	PACSIN3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238200-47241000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:47238200-47241200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:47238400-47239400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:47238400-47239600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:47238400-47239600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:47238400-47239600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:47238400-47239600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr11:47238400-47239600	Weak transcription	Primary T cells from cord blood	blood
9	chr11:47238400-47239600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr11:47238400-47239600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr11:47238400-47239600	Genic enhancers	Fetal Intestine Small	intestine
12	chr11:47238400-47240200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:47238400-47241800	Weak transcription	Primary B cells from cord blood	blood
14	chr11:47238400-47242000	Weak transcription	K562	blood
15	chr11:47238400-47245000	Weak transcription	Fetal Kidney	kidney
16	chr11:47238400-47246200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr11:47238400-47246600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:47238400-47255800	Weak transcription	Brain Anterior Caudate	brain
19	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:47238600-47239400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:47238600-47239400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:47238600-47239400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr11:47238600-47239400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:47238600-47239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:47238600-47239400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:47238600-47239400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:47238600-47239400	Enhancers	Brain Germinal Matrix	brain
28	chr11:47238600-47239400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr11:47238600-47239400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:47238600-47239400	Weak transcription	Esophagus	oesophagus
31	chr11:47238600-47239400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:47238600-47239400	Weak transcription	Fetal Brain Female	brain
33	chr11:47238600-47239400	Weak transcription	Fetal Thymus	thymus
34	chr11:47238600-47239400	Weak transcription	NH-A	brain
35	chr11:47238600-47239400	Enhancers	NHDF-Ad	bronchial
36	chr11:47238600-47239600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:47238600-47239600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:47238600-47239600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr11:47238600-47239600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:47238600-47239600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:47238600-47239600	Weak transcription	Fetal Lung	lung
42	chr11:47238600-47239600	Weak transcription	Gastric	stomach
43	chr11:47238600-47239600	Weak transcription	Lung	lung
44	chr11:47238600-47239600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:47238600-47239600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:47238600-47239600	Weak transcription	Stomach Mucosa	stomach
47	chr11:47238600-47239600	Weak transcription	Thymus	Thymus
48	chr11:47238600-47239600	Weak transcription	A549	lung
49	chr11:47238600-47239600	Enhancers	HepG2	liver
50	chr11:47238600-47239600	Weak transcription	HSMMtube	muscle

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