Variant report

Variant	rs4437459
Chromosome Location	chr6:24856323-24856324
allele	G/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24855906..24856901-chr6:25017966..25018945,4	K562	blood:
2	chr6:24855588..24857199-chr6:24871445..24874017,2	K562	blood:
3	chr6:24855755..24858612-chr6:24860747..24863062,2	K562	blood:
4	chr6:24855908..24856523-chr6:25070777..25071542,2	MCF-7	breast:
5	chr16:22124056..22124556-chr6:24856022..24856664,2	MCF-7	breast:
6	chr6:24856035..24856908-chr6:25071041..25071669,3	MCF-7	breast:
7	chr6:24855866..24856430-chr6:25602285..25602795,2	K562	blood:
8	chr6:24855936..24856490-chr6:24992134..24992789,3	K562	blood:
9	chr6:24855976..24856788-chr6:24991509..24992791,3	MCF-7	breast:
10	chr6:24855912..24856897-chr6:25070777..25071655,5	K562	blood:
11	chr6:24855899..24856851-chr6:25017945..25018795,5	MCF-7	breast:
12	chr6:24847230..24849170-chr6:24856316..24857852,2	K562	blood:
13	chr6:24856039..24856860-chr6:24991781..24992759,3	MCF-7	breast:

No data

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2747666	0.84[ASW][hapmap];0.85[AMR][1000 genomes]
rs2817749	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4236033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236034	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4421189	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4537125	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711065	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711066	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712861	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62402000	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467333	0.85[JPT][hapmap];0.84[LWK][hapmap];0.83[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	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4437459	HIST1H3H	cis	cerebellum	SCAN
rs4437459	PGBD1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
2	chr6:24804800-24858200	Weak transcription	Gastric	stomach
3	chr6:24818800-24856400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:24832400-24859600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:24833000-24857800	Weak transcription	Brain Angular Gyrus	brain
6	chr6:24836000-24857200	Weak transcription	Fetal Brain Female	brain
7	chr6:24838000-24856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:24838200-24856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:24839600-24858800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:24840400-24856400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:24842400-24856600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:24843800-24858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:24843800-24879400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:24844200-24859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:24844600-24856600	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:24844600-24858200	Weak transcription	Right Ventricle	heart
17	chr6:24844600-24860200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:24844600-24873200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:24846200-24858200	Weak transcription	Esophagus	oesophagus
20	chr6:24846200-24873400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:24846800-24866000	Weak transcription	Fetal Intestine Small	intestine
22	chr6:24847000-24876600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:24847800-24856600	Weak transcription	Lung	lung
24	chr6:24848400-24857400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:24848400-24858200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:24848400-24860000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:24848600-24859600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:24849000-24864600	Weak transcription	Brain Germinal Matrix	brain
29	chr6:24849200-24858200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr6:24850000-24858000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:24850400-24858800	Weak transcription	Liver	Liver
32	chr6:24850800-24864600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:24851000-24858200	Weak transcription	Left Ventricle	heart
34	chr6:24853600-24857200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:24854200-24858000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:24854400-24858200	Genic enhancers	Primary B cells from cord blood	blood
37	chr6:24854400-24869400	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr6:24854600-24857800	Enhancers	Fetal Heart	heart
39	chr6:24854800-24856400	Enhancers	Fetal Muscle Leg	muscle
40	chr6:24854800-24856800	Enhancers	Fetal Muscle Trunk	muscle
41	chr6:24854800-24857200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:24854800-24857400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:24854800-24857400	Weak transcription	Thymus	Thymus
44	chr6:24854800-24858200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:24854800-24858400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:24855200-24857400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:24855200-24895000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr6:24855400-24858400	Genic enhancers	Primary T cells from cord blood	blood
49	chr6:24855600-24856400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:24855600-24856400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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