Variant report

Variant	rs6537808
Chromosome Location	chr1:114625602-114625603
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114621614..114625641-chr1:114627637..114630642,5	MCF-7	breast:
2	chr1:114623758..114625854-chr1:114633416..114636156,2	MCF-7	breast:
3	chr1:114614196..114617663-chr1:114624428..114628635,5	MCF-7	breast:
4	chr1:114621187..114625954-chr1:114630932..114635442,7	MCF-7	breast:
5	chr1:114621189..114624161-chr1:114624603..114627561,2	MCF-7	breast:
6	chr1:114620515..114623507-chr1:114624325..114627250,3	K562	blood:
7	chr1:114623233..114626213-chr1:114628057..114630881,2	MCF-7	breast:
8	chr1:114590926..114593498-chr1:114625359..114627730,2	MCF-7	breast:
9	chr1:114623967..114627228-chr1:114653926..114657100,3	K562	blood:

No data

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10858028	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330700	0.88[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1574509	1.00[CHD][hapmap]
rs1683252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2432	1.00[CHD][hapmap]
rs2774285	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2774291	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2938353	0.84[EUR][1000 genomes]
rs3007010	0.81[EUR][1000 genomes]
rs3007012	0.83[EUR][1000 genomes]
rs3007013	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4240537	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs514647	0.85[EUR][1000 genomes]
rs529171	0.85[EUR][1000 genomes]
rs548040	0.84[EUR][1000 genomes]
rs654819	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6674121	1.00[JPT][hapmap]
rs9429734	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6537808	DENND2C	cis	parietal	SCAN
rs6537808	CSDE1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114619200-114640200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114621800-114626200	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr1:114621800-114626600	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:114621800-114626600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:114621800-114626600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:114623200-114626000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:114623200-114626000	Enhancers	Fetal Lung	lung
8	chr1:114623600-114626000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:114623600-114626600	Enhancers	NHEK	skin
10	chr1:114623600-114629800	Weak transcription	Pancreas	Pancrea
11	chr1:114623800-114626400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:114623800-114626400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr1:114624400-114626400	Enhancers	H9 Cell Line	embryonic stem cell
14	chr1:114624400-114626600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:114624600-114626600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:114624600-114626600	Enhancers	HMEC	breast
17	chr1:114624800-114626000	Enhancers	Fetal Intestine Small	intestine
18	chr1:114624800-114626200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:114624800-114626400	Enhancers	Placenta	Placenta
20	chr1:114624800-114630800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:114625000-114631000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:114625200-114625800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:114625200-114626400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:114625400-114631200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:114625400-114631800	Weak transcription	Brain Germinal Matrix	brain
26	chr1:114625400-114639600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:114625400-114639800	Weak transcription	Right Atrium	heart
28	chr1:114625600-114631000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:114625600-114631600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links