Variant report

Variant	rs17363393
Chromosome Location	chr2:180006052-180006053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:180005469..180007805-chr2:180127766..180130374,2	MCF-7	breast:
2	chr2:180005225..180008035-chr2:180008843..180011202,2	K562	blood:

Variant related genes	Relation type
ENSG00000187231	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1048026	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10497533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11892241	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11900884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12105478	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap]
rs16866665	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16866673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17453976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17454192	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454458	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1838872	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2008215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2028906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4101465	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4499457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58582728	1.00[AFR][1000 genomes]
rs60072979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61179885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433759	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433766	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs879539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
4	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
5	chr2:179973400-180012600	Weak transcription	NHLF	lung
6	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
9	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:179980000-180038800	Weak transcription	HMEC	breast
11	chr2:179980000-180056800	Weak transcription	HSMM	muscle
12	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
14	chr2:179985800-180010200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:179991600-180007200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
18	chr2:179992200-180014600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:179995800-180016200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:179996200-180047600	Weak transcription	NH-A	brain
21	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
22	chr2:179999800-180009600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:180000600-180016200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:180000600-180016200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr2:180001200-180016200	Strong transcription	HepG2	liver
26	chr2:180001800-180009000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:180002000-180011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:180002400-180008600	Strong transcription	Adipose Nuclei	Adipose
29	chr2:180002400-180012800	Weak transcription	NHEK	skin
30	chr2:180002400-180016400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:180003000-180007400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:180003000-180007600	Strong transcription	Fetal Lung	lung
34	chr2:180003000-180009000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:180003200-180011400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:180003200-180011600	Weak transcription	A549	lung
37	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:180003400-180006400	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:180003800-180016200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:180004000-180006200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:180004000-180006400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:180004000-180008600	Strong transcription	Fetal Intestine Large	intestine
43	chr2:180004000-180008600	Strong transcription	Fetal Thymus	thymus
44	chr2:180004000-180008600	Strong transcription	Dnd41	blood
45	chr2:180004000-180009200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:180004200-180006200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr2:180004200-180008600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:180004400-180006200	Strong transcription	Fetal Brain Female	brain
49	chr2:180004400-180006200	Strong transcription	Gastric	stomach
50	chr2:180004400-180006800	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links