Variant report

Variant	rs56054049
Chromosome Location	chr7:99673359-99673360
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99672281..99674937-chr7:99777668..99780640,2	K562	blood:
2	chr7:99673231..99675072-chr7:100026135..100027945,2	K562	blood:
3	chr7:99612127..99613798-chr7:99673052..99674639,2	K562	blood:
4	chr7:99668310..99676246-chr7:99677185..99681836,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166526	Chromatin interaction
ENSG00000106261	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11558475	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11558476	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532238	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12673441	0.85[ASN][1000 genomes]
rs4308665	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4421299	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4727445	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729573	0.83[ASN][1000 genomes]
rs55969052	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60697181	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67091024	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67110214	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68038211	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72615158	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72615159	0.85[ASN][1000 genomes]
rs7780686	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7796006	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803317	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs941289	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56054049	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs56054049	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs56054049	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs56054049	TRIM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99661600-99675200	ZNF genes & repeats	A549	lung
2	chr7:99664600-99673600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:99665800-99673400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:99665800-99673600	ZNF genes & repeats	Fetal Stomach	stomach
5	chr7:99666000-99675000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
6	chr7:99666400-99674000	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr7:99666400-99677200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:99666400-99678000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:99666600-99674000	ZNF genes & repeats	Fetal Muscle Leg	muscle
10	chr7:99666800-99673400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
11	chr7:99666800-99673600	ZNF genes & repeats	HSMM	muscle
12	chr7:99666800-99673800	ZNF genes & repeats	GM12878-XiMat	blood
13	chr7:99666800-99674400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr7:99666800-99675200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr7:99666800-99677000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:99667000-99673400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
17	chr7:99667000-99673600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:99667400-99673400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:99667400-99673600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr7:99667400-99674400	Strong transcription	HepG2	liver
21	chr7:99667400-99675000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:99667400-99675000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
23	chr7:99667600-99673600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
24	chr7:99667600-99673600	ZNF genes & repeats	K562	blood
25	chr7:99667600-99675200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:99667800-99673400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:99669400-99674800	Strong transcription	Brain Substantia Nigra	brain
28	chr7:99669400-99675000	Strong transcription	Brain Angular Gyrus	brain
29	chr7:99669600-99675000	Strong transcription	Brain Cingulate Gyrus	brain
30	chr7:99669600-99675200	Strong transcription	Brain Anterior Caudate	brain
31	chr7:99669600-99677600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:99669800-99675000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:99670200-99673400	Strong transcription	Pancreatic Islets	Pancreatic Islet
34	chr7:99670200-99674000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:99670200-99675000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:99670200-99675200	Strong transcription	Right Ventricle	heart
37	chr7:99670200-99676600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr7:99670400-99673400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:99670400-99673800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:99670400-99674800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr7:99670400-99674800	Strong transcription	Colon Smooth Muscle	Colon
42	chr7:99670400-99675000	Strong transcription	Fetal Brain Male	brain
43	chr7:99670400-99675000	Strong transcription	Gastric	stomach
44	chr7:99670400-99675200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr7:99670400-99675200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr7:99670400-99676200	Strong transcription	Brain Hippocampus Middle	brain
47	chr7:99670400-99676400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:99670400-99676600	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr7:99670400-99677000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr7:99670600-99674600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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