Variant report

Variant	rs3845398
Chromosome Location	chr1:180530439-180530440
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: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10798776	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914030	0.83[ASN][1000 genomes]
rs10914031	0.95[ASN][1000 genomes]
rs10914033	0.95[ASN][1000 genomes]
rs12095304	0.95[ASN][1000 genomes]
rs1339725	0.97[ASN][1000 genomes]
rs4651069	0.89[ASN][1000 genomes]
rs4651070	1.00[ASN][1000 genomes]
rs58012939	0.95[ASN][1000 genomes]
rs58901111	0.95[ASN][1000 genomes]
rs73052310	0.95[ASN][1000 genomes]
rs7514062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7519288	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.90[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	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

No data

Chromatin state (count:38 , 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	chr1:180529600-180530600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:180529600-180532800	Enhancers	NHEK	skin
17	chr1:180530000-180530600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:180530000-180531600	Weak transcription	Fetal Brain Female	brain
19	chr1:180530000-180535000	Enhancers	Left Ventricle	heart
20	chr1:180530200-180530600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:180530200-180530600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:180530200-180530600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr1:180530200-180530800	Enhancers	Pancreas	Pancrea
24	chr1:180530200-180530800	Enhancers	Right Atrium	heart
25	chr1:180530200-180530800	Enhancers	Right Ventricle	heart
26	chr1:180530200-180531200	Enhancers	Fetal Heart	heart
27	chr1:180530200-180531200	Enhancers	Fetal Muscle Leg	muscle
28	chr1:180530200-180532600	Enhancers	Aorta	Aorta
29	chr1:180530400-180530600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:180530400-180530600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:180530400-180530600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:180530400-180530600	Enhancers	HepG2	liver
33	chr1:180530400-180530600	Enhancers	NHLF	lung
34	chr1:180530400-180530800	Flanking Active TSS	HSMM	muscle
35	chr1:180530400-180531000	Enhancers	Fetal Brain Male	brain
36	chr1:180530400-180531000	Enhancers	A549	lung
37	chr1:180530400-180531600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:180530400-180531800	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links