Variant report

Variant	rs4421299
Chromosome Location	chr7:99660148-99660149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99653111..99656050-chr7:99659743..99662367,2	K562	blood:
2	chr7:99656182..99658433-chr7:99660144..99662417,2	K562	blood:

Variant related genes	Relation type
ENSG00000166529	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11558475	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11558476	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532238	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673441	0.82[ASN][1000 genomes]
rs4308665	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4727445	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4729573	0.81[ASN][1000 genomes]
rs55969052	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56054049	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60697181	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6592	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67091024	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67110214	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68038211	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72615158	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72615159	0.82[ASN][1000 genomes]
rs7780686	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7796006	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7803317	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941289	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4421299	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs4421299	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs4421299	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs4421299	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs4421299	PVRIG	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99648400-99661400	Weak transcription	Small Intestine	intestine
2	chr7:99648400-99667600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:99648400-99667600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:99648400-99667600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:99648400-99667800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:99648400-99668000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:99648600-99660600	Weak transcription	HSMM	muscle
8	chr7:99648600-99663400	Weak transcription	Stomach Mucosa	stomach
9	chr7:99653400-99666400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:99653800-99660200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:99653800-99663000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:99653800-99663200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:99653800-99664200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:99653800-99667600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:99654000-99662200	Strong transcription	Fetal Stomach	stomach
16	chr7:99654000-99663600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:99654000-99663800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:99654000-99664000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:99654000-99668000	Strong transcription	Fetal Brain Female	brain
20	chr7:99654200-99663000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr7:99654200-99663600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:99654200-99666400	Strong transcription	Fetal Intestine Small	intestine
23	chr7:99654200-99667400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:99654400-99661600	Strong transcription	A549	lung
25	chr7:99654400-99662200	Strong transcription	Fetal Lung	lung
26	chr7:99654400-99662400	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr7:99654400-99663000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:99654400-99664000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr7:99654400-99667600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:99654400-99667600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:99654400-99667600	Strong transcription	Brain Germinal Matrix	brain
32	chr7:99654400-99668400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:99654600-99660200	Strong transcription	Brain Anterior Caudate	brain
34	chr7:99654600-99660200	Strong transcription	Lung	lung
35	chr7:99654600-99661400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:99654600-99661800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:99654600-99662000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:99654600-99662000	Strong transcription	Liver	Liver
39	chr7:99654600-99662600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:99654600-99662600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr7:99654600-99663000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:99654600-99663600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr7:99654600-99663600	Strong transcription	Brain Hippocampus Middle	brain
44	chr7:99654600-99663600	Strong transcription	Thymus	Thymus
45	chr7:99654600-99665600	Strong transcription	Dnd41	blood
46	chr7:99654600-99667600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:99654600-99667600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:99654600-99667800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:99654800-99662800	Strong transcription	Placenta	Placenta
50	chr7:99655000-99662000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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