Variant report

Variant	rs3843275
Chromosome Location	chr1:180530607-180530608
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180530082..180533605-chr1:180534162..180536876,3	K562	blood:
2	chr1:180511669..180514906-chr1:180530245..180533112,3	K562	blood:
3	chr1:180529943..180534795-chr1:180578153..180581956,5	K562	blood:
4	chr1:180530185..180532877-chr1:180542986..180545564,3	K562	blood:
5	chr1:180520741..180525768-chr1:180529838..180532812,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XPR1-2	chr1:180530380-180530828	XLOC_000477

No data

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10914036	0.86[CEU][hapmap];0.85[MKK][hapmap]
rs12039331	0.85[CEU][hapmap]
rs4651070	0.81[EUR][1000 genomes]
rs4652514	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697589	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513944	0.86[CEU][hapmap]
rs7535761	0.90[ASN][1000 genomes]
rs7541993	0.86[CEU][hapmap]
rs7546119	0.86[CEU][hapmap];0.85[MKK][hapmap]
rs7551178	0.86[CEU][hapmap]
rs7552084	0.81[CEU][hapmap]
rs946631	0.86[CEU][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3843275	RGS8	cis	cerebellum	SCAN
rs3843275	ACBD6	cis	parietal	SCAN
rs3843275	FAM163A	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180516600-180536800	Weak transcription	Psoas Muscle	Psoas
2	chr1:180525200-180534400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:180529000-180531800	Enhancers	K562	blood
4	chr1:180529200-180530800	Enhancers	Hela-S3	cervix
5	chr1:180529200-180530800	Enhancers	NH-A	brain
6	chr1:180529200-180531000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:180529200-180531000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:180529200-180531000	Enhancers	HMEC	breast
9	chr1:180529200-180532800	Enhancers	HSMMtube	muscle
10	chr1:180529200-180533000	Enhancers	Osteobl	bone
11	chr1:180529400-180530800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:180529400-180531000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:180529400-180531200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:180529400-180532800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:180529600-180532800	Enhancers	NHEK	skin
16	chr1:180530000-180531600	Weak transcription	Fetal Brain Female	brain
17	chr1:180530000-180535000	Enhancers	Left Ventricle	heart
18	chr1:180530200-180530800	Enhancers	Pancreas	Pancrea
19	chr1:180530200-180530800	Enhancers	Right Atrium	heart
20	chr1:180530200-180530800	Enhancers	Right Ventricle	heart
21	chr1:180530200-180531200	Enhancers	Fetal Heart	heart
22	chr1:180530200-180531200	Enhancers	Fetal Muscle Leg	muscle
23	chr1:180530200-180532600	Enhancers	Aorta	Aorta
24	chr1:180530400-180530800	Flanking Active TSS	HSMM	muscle
25	chr1:180530400-180531000	Enhancers	Fetal Brain Male	brain
26	chr1:180530400-180531000	Enhancers	A549	lung
27	chr1:180530400-180531600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:180530400-180531800	Weak transcription	Stomach Mucosa	stomach
29	chr1:180530600-180530800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr1:180530600-180531600	Weak transcription	NHLF	lung
31	chr1:180530600-180531800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:180530600-180531800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:180530600-180531800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:180530600-180532000	Weak transcription	HepG2	liver
35	chr1:180530600-180532400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links