Variant report

Variant	rs4456399
Chromosome Location	chr13:52313630-52313631
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	chr13:52024953..52028665-chr13:52311565..52316008,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1885855	0.90[ASN][1000 genomes]
rs1923874	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4533167	0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4943008	0.81[ASW][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.83[ASN][1000 genomes]
rs4943014	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561644	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7320201	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7327107	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7984225	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7988297	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7990679	0.80[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9285179	0.81[ASW][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.83[ASN][1000 genomes]
rs9526792	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535716	0.81[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9535720	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]
rs992583	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4456399	NCRNA00282	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52288400-52322200	Weak transcription	K562	blood
2	chr13:52296400-52322200	Weak transcription	Fetal Heart	heart
3	chr13:52298000-52322200	Weak transcription	Fetal Brain Female	brain
4	chr13:52300400-52322200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:52300600-52316000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr13:52300600-52321800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:52302200-52314000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:52302600-52313800	Weak transcription	Dnd41	blood
9	chr13:52303400-52315000	Weak transcription	Fetal Thymus	thymus
10	chr13:52304000-52320400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr13:52305000-52320400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr13:52305200-52320400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:52305400-52313800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr13:52305400-52315000	Weak transcription	Fetal Stomach	stomach
16	chr13:52305400-52321600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr13:52305400-52321800	Weak transcription	Gastric	stomach
18	chr13:52305600-52314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:52305800-52322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr13:52306000-52314200	Weak transcription	NHLF	lung
21	chr13:52306000-52317800	Weak transcription	Small Intestine	intestine
22	chr13:52306000-52322200	Weak transcription	Left Ventricle	heart
23	chr13:52306000-52322200	Weak transcription	Right Ventricle	heart
24	chr13:52306200-52321400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
26	chr13:52306400-52320400	Weak transcription	Aorta	Aorta
27	chr13:52308000-52313800	Weak transcription	Brain Hippocampus Middle	brain
28	chr13:52308000-52313800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr13:52308000-52314400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr13:52308000-52314400	Weak transcription	Fetal Intestine Large	intestine
31	chr13:52308000-52315200	Weak transcription	Lung	lung
32	chr13:52308000-52316000	Strong transcription	HepG2	liver
33	chr13:52308000-52319000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr13:52308000-52322200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr13:52308200-52313800	Weak transcription	A549	lung
36	chr13:52308200-52314400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr13:52308200-52316000	Weak transcription	Brain Anterior Caudate	brain
38	chr13:52308200-52322200	Weak transcription	Stomach Mucosa	stomach
39	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:52308400-52313800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr13:52308400-52316800	Strong transcription	NHEK	skin
42	chr13:52308400-52320200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr13:52308400-52321000	Weak transcription	Fetal Intestine Small	intestine
44	chr13:52308400-52326800	Weak transcription	Hela-S3	cervix
45	chr13:52308600-52321000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr13:52309800-52318400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:52309800-52320600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:52309800-52322200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr13:52310000-52313800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr13:52310000-52314800	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links