Variant report

Variant	rs3015312
Chromosome Location	chr1:59395120-59395121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59279498..59283509-chr1:59392349..59395635,3	MCF-7	breast:
2	chr1:59244053..59249750-chr1:59393075..59399809,12	K562	blood:
3	chr1:59392641..59396388-chr1:59399124..59401431,3	K562	blood:
4	chr1:59246732..59251125-chr1:59394532..59399253,8	MCF-7	breast:
5	chr1:59393493..59395224-chr1:59396747..59398606,2	MCF-7	breast:
6	chr1:59245645..59251479-chr1:59393366..59398471,10	MCF-7	breast:
7	chr1:59284595..59286940-chr1:59394772..59397437,2	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10158831	0.85[EUR][1000 genomes]
rs10889121	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207331	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12090072	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12122077	0.81[CHB][hapmap]
rs2038863	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2477745	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2716105	0.85[JPT][hapmap]
rs2716107	0.81[JPT][hapmap]
rs2716113	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2716115	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2716127	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764911	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2764914	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764915	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2764917	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2953376	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3015311	0.81[JPT][hapmap]
rs4528141	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4912382	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6677752	0.81[CHB][hapmap]
rs7528731	0.81[CHB][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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59385200-59397800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:59386600-59399800	Enhancers	Fetal Intestine Small	intestine
3	chr1:59388400-59397800	Weak transcription	NHLF	lung
4	chr1:59388600-59397800	Weak transcription	Lung	lung
5	chr1:59388800-59397800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:59388800-59398600	Weak transcription	Pancreas	Pancrea
7	chr1:59389000-59398800	Weak transcription	Right Atrium	heart
8	chr1:59389000-59407000	Weak transcription	Spleen	Spleen
9	chr1:59389200-59395400	Weak transcription	Fetal Thymus	thymus
10	chr1:59389200-59398600	Weak transcription	Psoas Muscle	Psoas
11	chr1:59389200-59401400	Weak transcription	Left Ventricle	heart
12	chr1:59390200-59399600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:59391200-59399600	Enhancers	Fetal Intestine Large	intestine
14	chr1:59391600-59396200	Enhancers	Duodenum Mucosa	Duodenum
15	chr1:59391800-59396600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:59392000-59397800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:59392000-59399600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:59392600-59395200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:59392600-59396200	Enhancers	HMEC	breast
20	chr1:59392600-59398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:59392600-59399400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:59393000-59396000	Enhancers	K562	blood
23	chr1:59393200-59398400	Weak transcription	Adipose Nuclei	Adipose
24	chr1:59393400-59395400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:59393400-59397600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:59393400-59398800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:59393600-59397600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:59393600-59398600	Weak transcription	Fetal Lung	lung
29	chr1:59393600-59400800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:59393600-59406800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:59393800-59395200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:59393800-59396000	Flanking Active TSS	Hela-S3	cervix
33	chr1:59393800-59398600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:59394000-59395200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:59394200-59395600	Enhancers	Colonic Mucosa	Colon
36	chr1:59394400-59395200	Weak transcription	Esophagus	oesophagus
37	chr1:59394400-59395800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:59394400-59396200	Bivalent Enhancer	HepG2	liver
39	chr1:59394400-59396600	Enhancers	Small Intestine	intestine
40	chr1:59394600-59395200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:59394600-59395400	Enhancers	Gastric	stomach
42	chr1:59394600-59395800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr1:59394600-59396000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:59394600-59396400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:59394800-59395400	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:59394800-59395600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:59394800-59396000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:59395000-59395400	Flanking Active TSS	NHEK	skin
49	chr1:59395000-59395800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:59395000-59395800	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links