Variant report

Variant	rs856657
Chromosome Location	chr1:120455918-120455919
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr1:120455624-120456004	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr1:120455642-120455979	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120455729..120458677-chr1:120465147..120468544,4	MCF-7	breast:
2	chr1:120454474..120456790-chr1:120460931..120463931,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261662	TF binding region
ENSG00000134250	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1353131	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2453041	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2453059	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2493412	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2641315	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[AMR][1000 genomes]
rs3862255	1.00[AMR][1000 genomes]
rs894078	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv533996	chr1:120359524-120471049	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv436325	chr1:120390914-120471049	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv547625	chr1:120422705-120466108	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv2610	chr1:120451060-120471049	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs856657	EMBP1	cis	lymphoblastoid	seeQTL
rs856657	ACOT2	trans	lymphoblastoid	seeQTL
rs856657	PPP4R4	trans	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120448200-120471000	Weak transcription	Right Atrium	heart
2	chr1:120448400-120457400	Weak transcription	Fetal Brain Female	brain
3	chr1:120448800-120456000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:120449000-120456600	Weak transcription	Aorta	Aorta
5	chr1:120449200-120457200	Weak transcription	Gastric	stomach
6	chr1:120449600-120456200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:120449600-120457800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:120450000-120473000	Strong transcription	HSMM	muscle
9	chr1:120450200-120456200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:120450200-120457800	Weak transcription	Colonic Mucosa	Colon
11	chr1:120450200-120458600	Weak transcription	HepG2	liver
12	chr1:120450400-120456800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:120450400-120456800	Weak transcription	Pancreas	Pancrea
14	chr1:120450800-120456600	Weak transcription	Thymus	Thymus
15	chr1:120451000-120456600	Weak transcription	Spleen	Spleen
16	chr1:120451000-120458400	Weak transcription	Small Intestine	intestine
17	chr1:120451000-120466800	Weak transcription	Fetal Brain Male	brain
18	chr1:120451400-120456600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:120451400-120457200	Weak transcription	Hela-S3	cervix
20	chr1:120451600-120480000	Weak transcription	Psoas Muscle	Psoas
21	chr1:120452000-120456600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:120452000-120485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:120452200-120456400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:120452600-120456000	Weak transcription	Fetal Kidney	kidney
25	chr1:120452600-120456600	Weak transcription	HUVEC	blood vessel
26	chr1:120452600-120457400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:120452600-120472800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:120452800-120456000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:120452800-120456600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:120452800-120457400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:120452800-120460000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:120453000-120473200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:120453000-120476400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:120453000-120483600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:120453200-120456200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:120453200-120457200	Weak transcription	NHEK	skin
37	chr1:120453200-120457400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:120453200-120458000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:120453200-120475600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:120453400-120457000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:120453400-120457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:120453400-120457400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:120453400-120472600	Strong transcription	Osteobl	bone
44	chr1:120453400-120476400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:120453600-120456000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:120453600-120456000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:120453600-120456400	Weak transcription	Ovary	ovary
48	chr1:120453600-120456600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:120453600-120456600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:120453600-120456800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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