Variant report

Variant	rs56077950
Chromosome Location	chr4:122721412-122721413
allele	C/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	JUN	chr4:122720661-122723088	K562	blood:	n/a	chr4:122722469-122722482
2	CUX1	chr4:122721331-122721525	K562	blood:	n/a	n/a
3	POLR2A	chr4:122721399-122722832	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:122721051-122722982	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:122721220-122723052	K562	blood:	n/a	n/a
6	IRF1	chr4:122721008-122723011	K562	blood:	n/a	chr4:122722326-122722340
7	POLR2A	chr4:122721312-122723213	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:122721264-122722767	GM12878	blood:	n/a	n/a
9	GATA1	chr4:122721390-122722881	PBDE	blood:	n/a	chr4:122722077-122722094
10	SPI1	chr4:122721373-122722749	GM12878	blood:	n/a	chr4:122722188-122722201
11	POLR2A	chr4:122721120-122723542	K562	blood:	n/a	n/a
12	POLR2A	chr4:122721120-122723027	GM12891	blood:	n/a	n/a
13	POLR2A	chr4:122721050-122722869	GM18505	blood:	n/a	n/a
14	MAZ	chr4:122721311-122721426	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:122719927..122724442-chr4:122741540..122746604,11	MCF-7	breast:
2	chr4:122720772..122725008-chr4:122725244..122729002,8	K562	blood:
3	chr4:122616868..122619074-chr4:122720747..122723892,4	MCF-7	breast:

Variant related genes	Relation type
EXOSC9	TF binding region
ENSG00000145386	Chromatin interaction
ENSG00000164111	Chromatin interaction
ENSG00000123737	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11098645	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098646	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098648	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731570	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731917	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512876	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1396080	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1507994	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507995	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452156	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063165	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071486	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2221628	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3217753	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217771	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217773	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217780	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828485	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924987	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4077102	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516739	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56159666	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56311153	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58649165	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61217486	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534323	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67772833	0.92[EUR][1000 genomes]
rs6813653	0.81[ASN][1000 genomes]
rs6815790	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821305	0.90[ASN][1000 genomes]
rs6823818	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824258	0.80[ASN][1000 genomes]
rs6826506	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855269	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680779	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660548	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686084	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686200	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691955	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs769238	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769246	0.89[EUR][1000 genomes]
rs7699776	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684587	0.93[EUR][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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56077950	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122711800-122721800	Weak transcription	Fetal Stomach	stomach
2	chr4:122711800-122721800	Weak transcription	HMEC	breast
3	chr4:122712200-122721600	Weak transcription	A549	lung
4	chr4:122714600-122721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:122715600-122721800	Enhancers	Fetal Thymus	thymus
6	chr4:122716200-122721800	Weak transcription	Osteobl	bone
7	chr4:122716800-122721600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:122717000-122721800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:122717400-122721800	Weak transcription	NHEK	skin
10	chr4:122717600-122721600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:122717600-122721800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:122717600-122721800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:122717600-122721800	Weak transcription	Fetal Lung	lung
14	chr4:122717600-122721800	Weak transcription	NH-A	brain
15	chr4:122717600-122721800	Weak transcription	NHLF	lung
16	chr4:122717600-122722000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:122717800-122721600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:122717800-122721800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:122717800-122721800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:122717800-122721800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:122717800-122721800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:122717800-122721800	Weak transcription	HUVEC	blood vessel
23	chr4:122718000-122721800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:122718000-122721800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:122718200-122721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:122718200-122721800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:122718200-122721800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:122718200-122721800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:122718200-122721800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:122718200-122721800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:122719400-122721600	Enhancers	Dnd41	blood
32	chr4:122720000-122721600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:122720400-122721600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:122720400-122721600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr4:122720400-122721800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr4:122720400-122722000	Flanking Active TSS	HepG2	liver
37	chr4:122720400-122722200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr4:122720600-122721600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:122720600-122721600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr4:122720600-122721600	Flanking Active TSS	GM12878-XiMat	blood
41	chr4:122720600-122721800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:122720600-122721800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr4:122720600-122721800	Enhancers	HSMM	muscle
44	chr4:122720600-122721800	Enhancers	NHDF-Ad	bronchial
45	chr4:122720800-122721600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr4:122720800-122721800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:122720800-122721800	Enhancers	Fetal Intestine Large	intestine
48	chr4:122721000-122721600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr4:122721000-122721600	Enhancers	Fetal Intestine Small	intestine
50	chr4:122721000-122721800	Enhancers	HSMMtube	muscle

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