Variant report

Variant	rs2844659
Chromosome Location	chr6:30824532-30824533
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	chr6:30823525..30825673-chr6:30833056..30834672,2	K562	blood:
2	chr6:30582957..30586155-chr6:30822684..30826202,3	K562	blood:

Variant related genes	Relation type
ENSG00000204568	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10947109	0.81[ASN][1000 genomes]
rs11759918	0.92[ASN][1000 genomes]
rs1264318	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264319	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17189749	0.81[ASN][1000 genomes]
rs17840009	0.92[ASN][1000 genomes]
rs2517576	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535333	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2894054	0.83[ASN][1000 genomes]
rs45627239	0.81[ASN][1000 genomes]
rs55697712	0.81[ASN][1000 genomes]
rs59124304	0.81[ASN][1000 genomes]
rs6940037	0.81[ASN][1000 genomes]
rs73727104	0.81[ASN][1000 genomes]
rs73727106	0.81[ASN][1000 genomes]
rs73727107	0.89[ASN][1000 genomes]
rs73727480	0.83[ASN][1000 genomes]
rs7761138	0.89[ASN][1000 genomes]
rs7772269	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv884108	chr6:30821187-30838497	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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 miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2844659	VARS2	cis	lymphoblastoid	seeQTL
rs2844659	HIST1H2AM	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30816200-30824600	Weak transcription	Fetal Kidney	kidney
2	chr6:30820600-30824800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:30820600-30825000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:30821600-30825000	Enhancers	Placenta	Placenta
5	chr6:30822800-30825200	Enhancers	Fetal Intestine Large	intestine
6	chr6:30823200-30825200	Enhancers	Fetal Intestine Small	intestine
7	chr6:30823200-30826400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:30823400-30825400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:30823600-30826400	Enhancers	Fetal Thymus	thymus
10	chr6:30823600-30835400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:30823800-30824600	Flanking Bivalent TSS/Enh	HepG2	liver
12	chr6:30824000-30825200	Enhancers	GM12878-XiMat	blood
13	chr6:30824200-30825000	Enhancers	Fetal Brain Male	brain
14	chr6:30824200-30825400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:30824400-30826000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:30824400-30826200	Enhancers	Fetal Lung	lung

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