Variant report

Variant	rs4466281
Chromosome Location	chr6:4023950-4023951
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	ZNF384	chr6:4023938-4024268	GM12878	blood:	n/a	n/a
2	MAX	chr6:4023921-4024182	K562	blood:	n/a	n/a
3	ZNF384	chr6:4023867-4024273	K562	blood:	n/a	n/a
4	CHD1	chr6:4021012-4024108	IMR90	lung:	n/a	chr6:4021945-4021955
5	IRF1	chr6:4023506-4024527	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
2	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:
3	chr6:4019656..4024130-chr6:4049502..4053557,5	K562	blood:
4	chr6:3161756..3164171-chr6:4023037..4024626,2	K562	blood:
5	chr6:3354766..3356285-chr6:4022348..4024808,2	K562	blood:

Variant related genes	Relation type
ENSG00000230648	TF binding region
ENSG00000112739	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000145975	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000254821	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12174184	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408457	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543355	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1969837	0.82[EUR][1000 genomes]
rs2181894	0.95[ASN][1000 genomes]
rs2745451	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3747761	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747762	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747763	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761787	0.98[ASN][1000 genomes]
rs4959916	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959918	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959919	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6900476	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905475	0.83[ASN][1000 genomes]
rs6906467	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910519	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916982	0.95[ASN][1000 genomes]
rs6921738	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930892	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933593	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6941706	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs697745	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707980	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707981	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707982	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707983	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707984	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707985	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707987	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs707988	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73349780	0.84[ASN][1000 genomes]
rs7744603	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7763233	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853396	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853397	0.93[ASN][1000 genomes]
rs853398	0.94[ASN][1000 genomes]
rs853399	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853400	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853402	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853403	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853404	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853405	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853406	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853407	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853408	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853409	0.81[ASN][1000 genomes]
rs853410	0.83[ASN][1000 genomes]
rs853411	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs860477	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860478	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9328215	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328216	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9405694	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941443	0.95[ASN][1000 genomes]
rs942474	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503893	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4020800-4024000	Active TSS	HMEC	breast
2	chr6:4021000-4025000	Active TSS	GM12878-XiMat	blood
3	chr6:4021000-4025200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:4021200-4024200	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr6:4022200-4024000	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr6:4022400-4024000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:4022400-4024000	Weak transcription	Lung	lung
8	chr6:4022400-4024000	Weak transcription	Spleen	Spleen
9	chr6:4022400-4024200	Weak transcription	Gastric	stomach
10	chr6:4022400-4025600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:4022400-4028400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:4022400-4043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:4022600-4024000	Flanking Active TSS	Dnd41	blood
14	chr6:4022600-4024400	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr6:4022600-4049400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:4022800-4024000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr6:4022800-4024200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:4022800-4024600	Enhancers	Small Intestine	intestine
19	chr6:4023000-4024000	Weak transcription	Esophagus	oesophagus
20	chr6:4023000-4024000	Transcr. at gene 5' and 3'	K562	blood
21	chr6:4023000-4024200	Enhancers	Fetal Heart	heart
22	chr6:4023000-4024400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:4023000-4024600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:4023000-4025800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr6:4023000-4027000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr6:4023000-4027000	Weak transcription	Left Ventricle	heart
27	chr6:4023000-4028400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:4023000-4028400	Weak transcription	Ovary	ovary
29	chr6:4023000-4032000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:4023000-4038600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:4023200-4024000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:4023200-4024000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:4023200-4024000	Weak transcription	Right Ventricle	heart
35	chr6:4023200-4024200	Enhancers	Fetal Stomach	stomach
36	chr6:4023200-4024400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:4023200-4024600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:4023200-4024600	Enhancers	Fetal Muscle Leg	muscle
39	chr6:4023200-4024600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr6:4023200-4025800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:4023200-4027600	Weak transcription	Brain Angular Gyrus	brain
42	chr6:4023200-4028400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:4023200-4031800	Weak transcription	Placenta	Placenta
44	chr6:4023200-4034000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:4023200-4035600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:4023200-4043400	Weak transcription	Aorta	Aorta
47	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:4023400-4024000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:4023400-4024000	Enhancers	Primary B cells from cord blood	blood
50	chr6:4023400-4024000	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links