Variant report

Variant	rs4656339
Chromosome Location	chr1:161915387-161915388
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161908780..161912195-chr1:161914395..161917998,3	MCF-7	breast:
2	chr1:161903370..161905220-chr1:161914130..161916639,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10733044	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737502	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10753645	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753666	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800068	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394070	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553444	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1806594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134690	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2134696	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2298019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2341468	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2341479	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2499856	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2880055	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312480	1.00[ASN][1000 genomes]
rs34461550	0.90[ASN][1000 genomes]
rs35621393	0.94[ASN][1000 genomes]
rs36080602	1.00[ASN][1000 genomes]
rs3767633	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300199	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4579731	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4656335	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4657103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6427633	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427639	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667896	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685369	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6698065	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs71639910	0.98[ASN][1000 genomes]
rs7517386	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532448	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924777	0.88[AMR][1000 genomes];1.00[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	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4656339	FCGR2B	cis	multi-tissue	Pritchard
rs4656339	PEA15	cis	parietal	SCAN
rs4656339	TAGLN2	cis	cerebellum	SCAN
rs4656339	FCRLM2	cis	multi-tissue	Pritchard
rs4656339	NTRK1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161824200-161928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:161861600-161936000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:161883200-161916000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:161883400-161928200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:161884600-161927600	Weak transcription	NHEK	skin
6	chr1:161884800-161922600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:161885000-161928000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:161885800-161919200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:161887000-161918600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:161887000-161928200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:161887200-161915600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:161887200-161929600	Weak transcription	Hela-S3	cervix
13	chr1:161891000-161915600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:161891800-161915800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:161896200-161916400	Weak transcription	Fetal Stomach	stomach
16	chr1:161897800-161928400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:161897800-161940000	Weak transcription	Brain Germinal Matrix	brain
18	chr1:161899800-161918400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:161900000-161916000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:161900200-161918600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:161900600-161915600	Weak transcription	HSMM	muscle
22	chr1:161900600-161915600	Weak transcription	NHLF	lung
23	chr1:161901400-161935400	Weak transcription	Fetal Lung	lung
24	chr1:161902400-161923000	Weak transcription	Brain Substantia Nigra	brain
25	chr1:161902800-161943400	Weak transcription	Esophagus	oesophagus
26	chr1:161903600-161930400	Weak transcription	Fetal Brain Female	brain
27	chr1:161903800-161918800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:161903800-161923800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:161904400-161915600	Weak transcription	HSMMtube	muscle
30	chr1:161904400-161923200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
32	chr1:161905000-161920600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:161906000-161923200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:161906000-161923200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:161906000-161927800	Weak transcription	Thymus	Thymus
36	chr1:161906800-161918000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:161906800-161923200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:161906800-161928000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:161906800-161932200	Weak transcription	Stomach Mucosa	stomach
40	chr1:161907000-161919200	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:161907000-161923200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:161908400-161915400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:161910600-161915800	Strong transcription	Primary B cells from cord blood	blood
44	chr1:161910600-161922600	Weak transcription	Brain Angular Gyrus	brain
45	chr1:161911000-161937200	Weak transcription	Gastric	stomach
46	chr1:161911200-161915600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:161911200-161916000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:161911400-161917000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:161911400-161919400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:161911600-161915400	Strong transcription	Primary hematopoietic stem cells	blood

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