Variant report

Variant	rs2493397
Chromosome Location	chr1:120449627-120449628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120449201..120451980-chr1:120452971..120455460,2	MCF-7	breast:
2	chr1:120447256..120450228-chr1:120525932..120527487,2	K562	blood:
3	chr1:120445705..120448547-chr1:120448757..120452152,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261662	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs17024243	1.00[EUR][1000 genomes]
rs17024274	1.00[EUR][1000 genomes]
rs2453043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453057	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2453060	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2493393	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2493395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2493399	1.00[EUR][1000 genomes]
rs2493409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2641341	1.00[EUR][1000 genomes]
rs2691751	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2793828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2793924	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34996202	1.00[EUR][1000 genomes]
rs4274109	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59055697	1.00[EUR][1000 genomes]
rs60594933	1.00[EUR][1000 genomes]
rs6673881	1.00[EUR][1000 genomes]
rs6689706	1.00[EUR][1000 genomes]
rs6690032	1.00[EUR][1000 genomes]
rs6697236	1.00[EUR][1000 genomes]
rs74115097	1.00[EUR][1000 genomes]
rs74115360	1.00[EUR][1000 genomes]
rs74115365	1.00[EUR][1000 genomes]
rs7536072	1.00[EUR][1000 genomes]
rs7537153	1.00[EUR][1000 genomes]
rs7537385	1.00[EUR][1000 genomes]
rs7540526	1.00[EUR][1000 genomes]
rs835566	1.00[EUR][1000 genomes]
rs835567	1.00[EUR][1000 genomes]
rs835577	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120444600-120453000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:120446400-120452000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:120446400-120454400	Weak transcription	NH-A	brain
4	chr1:120446600-120453400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:120448200-120452600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:120448200-120471000	Weak transcription	Right Atrium	heart
7	chr1:120448400-120453200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:120448400-120457400	Weak transcription	Fetal Brain Female	brain
9	chr1:120448800-120454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:120448800-120455800	Weak transcription	NHLF	lung
11	chr1:120448800-120456000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:120449000-120456600	Weak transcription	Aorta	Aorta
13	chr1:120449200-120450000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:120449200-120450000	Weak transcription	HSMM	muscle
15	chr1:120449200-120450400	Enhancers	Pancreas	Pancrea
16	chr1:120449200-120450600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:120449200-120450600	Enhancers	Liver	Liver
18	chr1:120449200-120452800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:120449200-120457200	Weak transcription	Gastric	stomach
20	chr1:120449400-120450000	Weak transcription	Fetal Stomach	stomach
21	chr1:120449400-120450200	Enhancers	HepG2	liver
22	chr1:120449400-120450400	Enhancers	Fetal Intestine Large	intestine
23	chr1:120449400-120453000	Weak transcription	Esophagus	oesophagus
24	chr1:120449400-120453400	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:120449600-120450400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:120449600-120456200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:120449600-120457800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links