Variant report

Variant	rs56353092
Chromosome Location	chr4:16219216-16219217
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	SPI1	chr4:16218846-16219371	HL-60	blood:	n/a	chr4:16219109-16219122 chr4:16219010-16219023 chr4:16219110-16219123
2	NFATC1	chr4:16218812-16219358	GM12878	blood:	n/a	n/a
3	BATF	chr4:16218896-16219233	GM12878	blood:	n/a	n/a
4	SPI1	chr4:16218923-16219236	GM12878	blood:	n/a	chr4:16219109-16219122 chr4:16219010-16219023 chr4:16219110-16219123
5	SPI1	chr4:16218943-16219248	GM12891	blood:	n/a	chr4:16219109-16219122 chr4:16219010-16219023 chr4:16219110-16219123
6	SPI1	chr4:16218835-16219318	GM12891	blood:	n/a	chr4:16219109-16219122 chr4:16219010-16219023 chr4:16219110-16219123
7	CUX1	chr4:16218999-16219510	GM12878	blood:	n/a	n/a
8	NFATC1	chr4:16218855-16219359	GM12878	blood:	n/a	n/a
9	BCL11A	chr4:16218996-16219230	GM12878	blood:	n/a	n/a
10	SPI1	chr4:16218792-16219383	HL-60	blood:	n/a	chr4:16219109-16219122 chr4:16219010-16219023 chr4:16219110-16219123
11	BATF	chr4:16218958-16219224	GM12878	blood:	n/a	n/a
12	RUNX3	chr4:16218801-16219433	GM12878	blood:	n/a	n/a
13	SPI1	chr4:16218588-16219510	GM12878	blood:	n/a	chr4:16219109-16219122 chr4:16219010-16219023 chr4:16219110-16219123
14	REST	chr4:16219005-16219243	Hela-S3	cervix:	n/a	n/a
15	RUNX3	chr4:16218901-16219385	GM12878	blood:	n/a	n/a
16	NFIC	chr4:16218662-16219517	GM12878	blood:	n/a	n/a
17	IRF4	chr4:16218932-16219348	GM12878	blood:	n/a	n/a
18	NFIC	chr4:16218848-16219416	GM12878	blood:	n/a	n/a
19	SPI1	chr4:16218970-16219239	GM12878	blood:	n/a	chr4:16219109-16219122 chr4:16219010-16219023 chr4:16219110-16219123
20	FOXM1	chr4:16218845-16219384	GM12878	blood:	n/a	n/a
21	ATF2	chr4:16218861-16219407	GM12878	blood:	n/a	n/a
22	EP300	chr4:16218987-16219289	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:
2	chr4:16214884..16216765-chr4:16218812..16220589,2	K562	blood:
3	chr4:16218843..16221632-chr4:16227954..16229543,2	K562	blood:

Variant related genes	Relation type
TAPT1	TF binding region
ENSG00000263327	Chromatin interaction
ENSG00000169762	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10516297	0.92[ASN][1000 genomes]
rs11730922	0.92[ASN][1000 genomes]
rs13110290	0.84[ASN][1000 genomes]
rs13120908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13132678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13136055	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13136172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028631	0.83[ASN][1000 genomes]
rs28654954	0.80[ASN][1000 genomes]
rs2872216	0.93[ASN][1000 genomes]
rs33980476	0.87[ASN][1000 genomes]
rs34129131	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34496855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34592687	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34663238	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34837883	0.95[EUR][1000 genomes]
rs35475888	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35517826	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35804424	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35806798	0.96[ASN][1000 genomes]
rs35899968	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35931597	0.82[ASN][1000 genomes]
rs3749544	0.94[ASN][1000 genomes]
rs4235382	0.83[ASN][1000 genomes]
rs4481232	0.84[ASN][1000 genomes]
rs4571326	0.84[ASN][1000 genomes]
rs4698457	0.86[ASN][1000 genomes]
rs6810390	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823229	0.92[ASN][1000 genomes]
rs6823230	0.92[ASN][1000 genomes]
rs6852432	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9995025	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56353092	TAPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16181200-16223800	Weak transcription	Fetal Brain Male	brain
2	chr4:16193000-16225800	Weak transcription	Colonic Mucosa	Colon
3	chr4:16193200-16225800	Weak transcription	Fetal Brain Female	brain
4	chr4:16198600-16221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:16198600-16222400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:16198800-16225600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:16198800-16226000	Weak transcription	NHEK	skin
8	chr4:16198800-16226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:16202800-16220800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:16204800-16226600	Weak transcription	NH-A	brain
11	chr4:16205200-16225600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:16207400-16223600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:16208400-16224400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:16208400-16225200	Weak transcription	Fetal Kidney	kidney
15	chr4:16208400-16225800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:16208800-16225600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:16208800-16225600	Weak transcription	Esophagus	oesophagus
18	chr4:16208800-16225600	Weak transcription	Gastric	stomach
19	chr4:16208800-16225800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:16208800-16225800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:16208800-16227200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:16209000-16225600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:16209200-16223400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:16209200-16225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:16209200-16225600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:16209400-16226200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:16209400-16226200	Weak transcription	HSMMtube	muscle
28	chr4:16209600-16221400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:16210400-16225800	Weak transcription	Brain Germinal Matrix	brain
30	chr4:16212000-16220600	Weak transcription	A549	lung
31	chr4:16212200-16226000	Weak transcription	NHDF-Ad	bronchial
32	chr4:16213000-16221400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:16214000-16224400	Weak transcription	Brain Anterior Caudate	brain
34	chr4:16214200-16221800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr4:16214200-16224200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:16214400-16220800	Weak transcription	Fetal Stomach	stomach
37	chr4:16214400-16226800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:16214600-16222600	Weak transcription	Fetal Heart	heart
39	chr4:16214600-16224400	Weak transcription	Brain Angular Gyrus	brain
40	chr4:16214600-16225800	Weak transcription	Placenta	Placenta
41	chr4:16214800-16220800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr4:16214800-16224200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:16214800-16225200	Weak transcription	Hela-S3	cervix
44	chr4:16214800-16225800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:16215000-16220200	Weak transcription	K562	blood
46	chr4:16215000-16220800	Weak transcription	Fetal Intestine Large	intestine
47	chr4:16215000-16221000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:16215000-16223600	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:16215000-16224600	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:16215000-16226000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links