Variant report

Variant	rs1770342
Chromosome Location	chr6:15089309-15089310
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:15085986..15094450-chr6:15243173..15249347,32	MCF-7	breast:
2	chr6:15088454..15091086-chr6:32937354..32938883,2	MCF-7	breast:
3	chr6:15088518..15090840-chr6:15243708..15248817,8	MCF-7	breast:
4	chr6:15060990..15063217-chr6:15088088..15090210,2	MCF-7	breast:
5	chr6:15087697..15090095-chr6:15243505..15246959,6	K562	blood:
6	chr6:15087697..15092455-chr6:15243972..15249952,11	K562	blood:
7	chr6:14725985..14728380-chr6:15088035..15090181,2	K562	blood:
8	chr6:15087836..15090279-chr6:15247303..15249952,4	K562	blood:
9	chr10:5507144..5509626-chr6:15088279..15090071,2	MCF-7	breast:
10	chr6:15088011..15090050-chr6:15218799..15221115,2	MCF-7	breast:
11	chr6:15088400..15090087-chr6:15163313..15165658,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000271888	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1622305	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1770341	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2010233	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2144159	0.82[CEU][hapmap]
rs2327849	0.80[YRI][hapmap]
rs2474107	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2747484	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2747485	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2747487	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2747488	0.86[ASN][1000 genomes]
rs2747496	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs2747500	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs2791608	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2791611	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3935737	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62397260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753952	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830593	chr6:15049636-15244190	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1770342	FLJ13224	trans	parietal	SCAN
rs1770342	GFOD1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15077000-15090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:15080000-15089400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:15083800-15093000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:15087200-15091600	Enhancers	Placenta	Placenta
5	chr6:15087400-15090000	Weak transcription	Primary B cells from cord blood	blood
6	chr6:15087400-15117600	Weak transcription	Right Atrium	heart
7	chr6:15087600-15090200	Weak transcription	Fetal Thymus	thymus
8	chr6:15087800-15089400	Weak transcription	Stomach Mucosa	stomach
9	chr6:15087800-15090000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:15087800-15090000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:15088200-15089400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:15088200-15089800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:15088400-15089800	Active TSS	K562	blood
14	chr6:15088800-15090000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:15089000-15089400	Enhancers	Fetal Kidney	kidney
16	chr6:15089000-15089600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:15089000-15091800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:15089200-15089400	Enhancers	Duodenum Mucosa	Duodenum
19	chr6:15089200-15089600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:15089200-15090000	Enhancers	Fetal Stomach	stomach
21	chr6:15089200-15091000	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links