Variant report

Variant	rs6869909
Chromosome Location	chr5:76163813-76163814
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:76163760..76164637-chr5:76311217..76312283,3	MCF-7	breast:
2	chr5:76163632..76164571-chr5:76382049..76382765,2	MCF-7	breast:
3	chr5:76163387..76165111-chr5:76366962..76369589,2	K562	blood:
4	chr5:76163515..76164197-chr5:76787927..76788778,2	K562	blood:
5	chr5:76162914..76165922-chr5:76372633..76374807,3	K562	blood:
6	chr5:76163711..76164616-chr5:76311702..76312587,6	MCF-7	breast:
7	chr5:76163618..76164624-chr5:76373134..76374055,4	K562	blood:
8	chr5:76163643..76164600-chr5:76311594..76312851,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164253	Chromatin interaction
ENSG00000250802	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10055746	1.00[ASN][1000 genomes]
rs10063816	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10070865	0.88[CEU][hapmap]
rs10076411	1.00[ASN][1000 genomes]
rs10440683	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10440684	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10462547	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10462548	0.96[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs12152714	0.99[ASN][1000 genomes]
rs12152998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12188004	0.84[TSI][hapmap]
rs12519617	0.80[TSI][hapmap]
rs12653515	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13160667	0.98[ASN][1000 genomes]
rs13168922	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1320306	0.80[TSI][hapmap]
rs1320308	0.84[CEU][hapmap]
rs1320309	0.92[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs1343712	0.99[ASN][1000 genomes]
rs2359427	0.80[CEU][hapmap]
rs2359658	0.81[GIH][hapmap];0.84[TSI][hapmap]
rs55863251	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414971	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6453259	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6453260	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6859961	0.99[ASN][1000 genomes]
rs6860303	0.99[ASN][1000 genomes]
rs6874234	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736104	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9293697	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9293698	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9885484	1.00[CHB][hapmap];1.00[JPT][hapmap];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	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3393424	chr5:76122720-76287744	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv34133	chr5:76138696-76239330	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6869909	F2RL1	cis	multi-tissue	Pritchard
rs6869909	CRHBP	cis	Esophagus Muscularis	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76153000-76174400	Weak transcription	Primary T cells from cord blood	blood
2	chr5:76158400-76165200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:76159000-76169600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:76162200-76164200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:76162800-76164000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:76162800-76164000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:76162800-76164600	Enhancers	Primary hematopoietic stem cells	blood
8	chr5:76163000-76164000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:76163000-76164000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:76163000-76164000	Enhancers	Hela-S3	cervix
11	chr5:76163400-76164600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr5:76163400-76164600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:76163400-76164600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr5:76163400-76164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:76163600-76164000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:76163600-76164000	Enhancers	Duodenum Mucosa	Duodenum
17	chr5:76163600-76164000	Enhancers	Fetal Heart	heart
18	chr5:76163600-76164000	Enhancers	Fetal Intestine Small	intestine
19	chr5:76163600-76164000	Enhancers	Stomach Mucosa	stomach
20	chr5:76163600-76164000	Flanking Active TSS	A549	lung
21	chr5:76163600-76164000	Enhancers	HMEC	breast
22	chr5:76163800-76164000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:76163800-76164000	Enhancers	Brain Anterior Caudate	brain
24	chr5:76163800-76164000	Enhancers	Brain Cingulate Gyrus	brain
25	chr5:76163800-76164000	Enhancers	Brain Hippocampus Middle	brain
26	chr5:76163800-76164000	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr5:76163800-76164000	Enhancers	Brain Substantia Nigra	brain
28	chr5:76163800-76164000	Flanking Active TSS	HSMMtube	muscle
29	chr5:76163800-76164200	Enhancers	Brain Angular Gyrus	brain
30	chr5:76163800-76164400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:76163800-76171800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links