Variant report

Variant	rs753425
Chromosome Location	chr1:120316746-120316747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120315172..120317615-chr17:59486307..59488935,2	MCF-7	breast:
2	chr1:120315709..120317268-chr1:120336953..120338874,2	MCF-7	breast:
3	chr1:120307185..120310919-chr1:120314740..120318225,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000134240	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1163542	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1163543	0.97[EUR][1000 genomes]
rs1163544	0.96[EUR][1000 genomes]
rs1163550	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177389	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123085	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12132674	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660607	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1814447	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582779	0.97[EUR][1000 genomes]
rs2582780	0.97[EUR][1000 genomes]
rs2582782	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2582784	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2582785	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2582786	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582790	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2843014	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843015	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2843016	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239558	0.89[ASN][1000 genomes]
rs61789690	0.85[ASN][1000 genomes]
rs72695189	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs930448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935060	0.99[EUR][1000 genomes]
rs978730	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120311600-120318800	Enhancers	Fetal Intestine Large	intestine
2	chr1:120311800-120317800	Enhancers	HepG2	liver
3	chr1:120311800-120319600	Enhancers	Fetal Intestine Small	intestine
4	chr1:120311800-120324800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:120311800-120325400	Weak transcription	Lung	lung
6	chr1:120312000-120318600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:120313400-120317400	Enhancers	Fetal Lung	lung
8	chr1:120314400-120318000	Weak transcription	Colonic Mucosa	Colon
9	chr1:120314400-120322600	Weak transcription	Right Atrium	heart
10	chr1:120314600-120321800	Weak transcription	Fetal Stomach	stomach
11	chr1:120314600-120324800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:120315200-120317000	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:120315200-120318400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:120315400-120317000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:120315400-120318000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:120315600-120317800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:120315600-120318400	Enhancers	Stomach Mucosa	stomach
18	chr1:120315800-120316800	Enhancers	Placenta	Placenta
19	chr1:120315800-120316800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:120315800-120316800	Enhancers	Small Intestine	intestine
21	chr1:120315800-120317000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:120315800-120317200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr1:120315800-120317200	Enhancers	Fetal Heart	heart
24	chr1:120315800-120318200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:120315800-120322000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:120316000-120316800	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:120316000-120317000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr1:120316000-120317000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:120316000-120317000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:120316000-120317000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:120316000-120317000	Enhancers	HSMMtube	muscle
32	chr1:120316000-120317000	Enhancers	NHEK	skin
33	chr1:120316000-120317400	Enhancers	Fetal Kidney	kidney
34	chr1:120316200-120316800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:120316200-120316800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:120316200-120316800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:120316200-120316800	Enhancers	Esophagus	oesophagus
38	chr1:120316200-120316800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:120316200-120316800	Enhancers	Gastric	stomach
40	chr1:120316200-120316800	Enhancers	Left Ventricle	heart
41	chr1:120316200-120316800	Enhancers	Pancreas	Pancrea
42	chr1:120316200-120316800	Enhancers	Psoas Muscle	Psoas
43	chr1:120316200-120316800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:120316200-120316800	Flanking Active TSS	Hela-S3	cervix
45	chr1:120316200-120316800	Enhancers	NHDF-Ad	bronchial
46	chr1:120316200-120317000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:120316200-120317000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:120316200-120317000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:120316200-120317000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:120316200-120317000	Enhancers	Osteobl	bone

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