Variant report

Variant	rs853402
Chromosome Location	chr6:4054845-4054846
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:4054742-4054977	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:4054760..4058464-chr6:4059155..4063115,3	K562	blood:
2	chr6:4038778..4041215-chr6:4053376..4056511,3	K562	blood:
3	chr6:4046276..4049820-chr6:4052310..4055937,3	K562	blood:
4	chr6:4016440..4019187-chr6:4054276..4058013,4	K562	blood:
5	chr6:4050759..4052710-chr6:4054373..4057120,2	K562	blood:
6	chr6:4040702..4042424-chr6:4053690..4055352,2	MCF-7	breast:

No data

Variant related genes	Relation type
FAM217A	TF binding region
PRPF4B	TF binding region
ENSG00000112739	Chromatin interaction
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12174184	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1408457	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1543355	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2181894	0.86[ASN][1000 genomes]
rs2745451	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3747761	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747762	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747763	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3761787	0.92[ASN][1000 genomes]
rs4466281	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4959916	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4959918	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4959919	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6900476	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6905475	0.85[ASN][1000 genomes]
rs6906467	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6910519	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914180	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916982	0.86[ASN][1000 genomes]
rs6921738	0.84[ASN][1000 genomes]
rs6930892	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6933593	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6941706	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs697745	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707980	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707981	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707982	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707983	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707984	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707985	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707987	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs707988	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73349780	0.85[ASN][1000 genomes]
rs7744603	0.90[ASN][1000 genomes]
rs7763233	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853396	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853397	0.87[ASN][1000 genomes]
rs853398	0.96[ASN][1000 genomes]
rs853399	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853400	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs853403	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853404	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853405	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853406	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853407	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853408	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853409	0.86[ASN][1000 genomes]
rs853410	0.89[ASN][1000 genomes]
rs853411	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs860477	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860478	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9328215	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9328216	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9405694	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs941443	0.86[ASN][1000 genomes]
rs942474	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9503893	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1034223	chr6:4030708-4060347	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
4	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:4024600-4059200	Strong transcription	Fetal Thymus	thymus
6	chr6:4027200-4058200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:4030600-4065800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:4030800-4059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:4030800-4066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:4031000-4059200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:4031000-4066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:4031200-4066600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:4033400-4055200	Strong transcription	K562	blood
14	chr6:4034000-4066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:4035600-4063600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:4035600-4064200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr6:4035800-4057400	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:4035800-4058400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:4035800-4058600	Strong transcription	Primary T cells from cord blood	blood
20	chr6:4035800-4064600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:4035800-4065000	Strong transcription	Dnd41	blood
22	chr6:4035800-4066000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr6:4035800-4066000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr6:4035800-4066200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:4036000-4058200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:4036000-4066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:4036000-4066600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr6:4036400-4055200	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:4036600-4055200	Strong transcription	NHEK	skin
30	chr6:4037200-4059400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr6:4037200-4066200	Strong transcription	Liver	Liver
32	chr6:4037400-4055600	Strong transcription	Hela-S3	cervix
33	chr6:4037400-4058400	Strong transcription	HepG2	liver
34	chr6:4037400-4059400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:4037400-4065800	Strong transcription	Placenta	Placenta
36	chr6:4037600-4055400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:4037600-4066200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr6:4037600-4066400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr6:4037800-4058600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:4037800-4058600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:4037800-4058800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:4037800-4059400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:4038200-4058200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:4038800-4058200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:4038800-4066000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:4040000-4055200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:4040000-4055600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:4040000-4058600	Strong transcription	Colon Smooth Muscle	Colon
49	chr6:4040200-4058200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:4040800-4065400	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links