Variant report

Variant	rs4599669
Chromosome Location	chr6:133141291-133141292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:132935279..132937061-chr6:133139072..133141964,2	K562	blood:
2	chr6:133139865..133142318-chr6:133176855..133179137,2	K562	blood:
3	chr6:133139552..133142163-chr6:133253017..133254972,3	K562	blood:
4	chr6:132990956..132993235-chr6:133139715..133142471,3	K562	blood:
5	chr6:133139209..133141849-chr6:133290608..133292386,2	MCF-7	breast:
6	chr6:133140267..133142584-chr6:133384243..133385857,2	MCF-7	breast:
7	chr6:133139056..133141484-chr6:133198427..133200409,2	MCF-7	breast:
8	chr6:133139979..133142138-chr6:133214137..133215920,2	MCF-7	breast:
9	chr6:133140432..133142390-chr6:133219540..133222428,2	MCF-7	breast:
10	chr3:64145733..64148089-chr6:133139687..133142420,2	MCF-7	breast:
11	chr6:133140438..133142973-chr6:133152186..133155729,4	K562	blood:
12	chr11:18417141..18419717-chr6:133139653..133142088,2	K562	blood:
13	chr6:133139807..133142163-chr6:133253017..133254906,2	K562	blood:
14	chr6:132893374..132895125-chr6:133139533..133141338,2	K562	blood:
15	chr6:133072472..133075164-chr6:133139801..133141888,2	K562	blood:
16	chr6:133140710..133143536-chr6:133169760..133172712,2	K562	blood:
17	chr6:133008525..133010705-chr6:133141120..133143788,2	K562	blood:
18	chr6:133139563..133143378-chr6:133869645..133873437,4	K562	blood:
19	chr15:34330929..34333080-chr6:133140289..133142201,2	MCF-7	breast:
20	chr6:133140291..133143900-chr6:133848629..133850657,3	MCF-7	breast:
21	chr16:69363165..69365715-chr6:133141227..133142779,2	MCF-7	breast:
22	chr6:132849284..132852259-chr6:133140271..133142677,3	MCF-7	breast:
23	chr6:133139428..133141767-chr6:133455373..133456926,2	K562	blood:
24	chr6:133140672..133145394-chr6:133829879..133833202,4	K562	blood:
25	chr6:133140486..133142664-chr6:133322602..133325155,3	K562	blood:
26	chr6:133139605..133142425-chr6:133167716..133170536,3	MCF-7	breast:
27	chr6:133139130..133141825-chr6:133875719..133879392,4	MCF-7	breast:
28	chr6:133139381..133142834-chr6:134271951..134274965,4	K562	blood:
29	chr6:132976419..132978417-chr6:133140501..133142676,2	MCF-7	breast:
30	chr1:149223494..149225494-chr6:133139275..133142169,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction
ENSG00000258429	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000227954	Chromatin interaction
ENSG00000028839	Chromatin interaction
ENSG00000234484	Chromatin interaction
ENSG00000169857	Chromatin interaction
ENSG00000238059	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10457594	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11154696	0.91[MEX][hapmap]
rs12200907	0.82[CHD][hapmap]
rs12202302	0.85[CHB][hapmap];0.88[MEX][hapmap]
rs12206120	0.81[ASN][1000 genomes]
rs1359142	0.82[CHD][hapmap]
rs1408062	0.83[CHD][hapmap]
rs2236381	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs35893416	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756968	0.90[ASN][1000 genomes]
rs3778174	0.87[AFR][1000 genomes]
rs4897617	0.82[CHD][hapmap]
rs6569853	0.82[ASN][1000 genomes]
rs6569854	0.82[ASN][1000 genomes]
rs6920271	0.89[ASN][1000 genomes]
rs6926466	0.85[CHB][hapmap];0.88[MEX][hapmap]
rs7452703	0.91[ASN][1000 genomes]
rs755895	0.81[ASN][1000 genomes]
rs761125	0.85[CHB][hapmap]
rs7751879	0.86[CEU][hapmap];0.85[CHB][hapmap]
rs7756588	0.83[CHD][hapmap]
rs7764152	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9321374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373030	0.83[CHD][hapmap]
rs9389034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9399044	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402457	0.89[ASN][1000 genomes]
rs9493450	0.83[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs9493451	0.90[CHB][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs9493458	0.86[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4599669	RPS12,SNORA33,SNORD100,SNORD101	cis	brain	BrainEAC
rs4599669	SNORA33	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133137200-133145400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:133137400-133141400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr6:133137800-133141400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:133137800-133141400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:133137800-133141600	Strong transcription	Fetal Thymus	thymus
6	chr6:133137800-133142200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:133137800-133142400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:133137800-133142400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr6:133137800-133143600	Weak transcription	Right Atrium	heart
10	chr6:133138000-133141400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:133138000-133141400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:133138000-133141400	Strong transcription	Colon Smooth Muscle	Colon
13	chr6:133138000-133141400	Strong transcription	Fetal Intestine Large	intestine
14	chr6:133138000-133141400	Strong transcription	Fetal Muscle Leg	muscle
15	chr6:133138000-133141600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr6:133138000-133141600	Strong transcription	Brain Cingulate Gyrus	brain
17	chr6:133138400-133141400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr6:133138400-133141400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:133138400-133141400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:133138400-133141600	Strong transcription	Fetal Stomach	stomach
21	chr6:133138400-133142400	Strong transcription	Primary B cells from cord blood	blood
22	chr6:133138400-133144400	Weak transcription	Stomach Mucosa	stomach
23	chr6:133138600-133141400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:133138600-133141400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr6:133138600-133142000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr6:133138600-133142400	Strong transcription	Fetal Brain Female	brain
27	chr6:133138600-133142600	Strong transcription	Primary T cells from cord blood	blood
28	chr6:133138800-133141400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:133138800-133142200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:133138800-133144400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:133139000-133141400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:133139000-133141400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:133139000-133142200	Strong transcription	Fetal Kidney	kidney
34	chr6:133139400-133141400	Strong transcription	Lung	lung
35	chr6:133139400-133142000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:133139400-133142000	Weak transcription	Hela-S3	cervix
37	chr6:133139400-133143400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:133139400-133146400	Weak transcription	Psoas Muscle	Psoas
39	chr6:133139600-133142000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:133139600-133142400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:133139600-133143400	Weak transcription	Esophagus	oesophagus
42	chr6:133139600-133144200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr6:133139600-133145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:133139800-133141400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:133139800-133141800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:133139800-133145400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:133140000-133141400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:133140200-133141600	Strong transcription	Fetal Brain Male	brain
49	chr6:133140200-133142200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr6:133140400-133141400	Strong transcription	Small Intestine	intestine

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