Variant report

Variant	rs73953291
Chromosome Location	chr2:127954990-127954991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:127825662..127826505-chr2:127954218..127955183,2	MCF-7	breast:
2	chr2:127918325..127921184-chr2:127953363..127955370,2	K562	blood:
3	chr2:127953428..127957461-chr2:128050157..128053368,5	MCF-7	breast:
4	chr2:127954513..127957323-chr2:128050197..128052990,3	MCF-7	breast:
5	chr2:127954454..127955271-chr2:128051262..128051788,2	MCF-7	breast:
6	chr2:127954574..127955249-chr2:128236342..128237229,4	MCF-7	breast:
7	chr2:127954775..127955774-chr2:128028067..128028796,3	MCF-7	breast:
8	chr2:127947734..127951220-chr2:127951984..127955891,4	MCF-7	breast:
9	chr2:127954460..127955590-chr2:128210604..128211170,3	K562	blood:
10	chr2:127954244..127955683-chr2:128210529..128212030,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs35075135	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55897983	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55912480	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56096327	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56911251	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953271	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953273	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953278	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953279	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953280	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953282	1.00[AMR][1000 genomes]
rs73953284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953287	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953292	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73953302	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956513	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956524	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73956527	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127934600-127955000	Weak transcription	NHEK	skin
2	chr2:127934600-127965600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:127941000-127963000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:127943000-127959400	Weak transcription	Gastric	stomach
5	chr2:127948600-127959400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:127948800-127973400	Weak transcription	HMEC	breast
7	chr2:127951200-127965800	Weak transcription	Esophagus	oesophagus
8	chr2:127951400-127962200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:127951600-127955200	Weak transcription	Psoas Muscle	Psoas
10	chr2:127951600-127958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:127952000-127963000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:127952200-127959000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:127952200-127964400	Weak transcription	Right Atrium	heart
14	chr2:127952200-127975200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:127952400-127955000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:127952400-127955600	Weak transcription	Fetal Kidney	kidney
17	chr2:127952400-127958800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:127952400-127959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:127953200-127955000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:127953200-127958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:127953600-127955000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:127953600-127955000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:127953600-127955200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:127953600-127955400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:127953600-127956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:127953600-127958200	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:127953600-127961000	Strong transcription	Fetal Stomach	stomach
28	chr2:127954200-127964000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:127954600-127955200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr2:127954600-127955400	Enhancers	Liver	Liver
31	chr2:127954600-127955400	Active TSS	GM12878-XiMat	blood
32	chr2:127954600-127957400	Strong transcription	Fetal Lung	lung
33	chr2:127954600-127962800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:127954800-127955000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr2:127954800-127955000	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr2:127954800-127955000	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr2:127954800-127955200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr2:127954800-127955200	Flanking Active TSS	HepG2	liver
39	chr2:127954800-127955400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr2:127954800-127955400	Flanking Active TSS	Hela-S3	cervix
41	chr2:127954800-127955600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:127954800-127955800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr2:127954800-127956000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:127954800-127960000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:127954800-127965600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links