Variant report

Variant	rs2920843
Chromosome Location	chr2:55338759-55338760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:
2	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
3	chr2:55275064..55278271-chr2:55336145..55339086,3	MCF-7	breast:
4	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12464094	1.00[AFR][1000 genomes]
rs2920872	1.00[AFR][1000 genomes]
rs2968807	1.00[AFR][1000 genomes]
rs2968812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2968813	1.00[AMR][1000 genomes]
rs2968814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2968816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972084	1.00[AFR][1000 genomes]
rs2972085	1.00[AMR][1000 genomes]
rs2972087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2972091	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006172	chr2:55322883-55340812	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv999212	chr2:55324276-55340812	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55321600-55339400	Weak transcription	Thymus	Thymus
2	chr2:55325200-55340400	Weak transcription	Gastric	stomach
3	chr2:55329600-55342600	Weak transcription	NHEK	skin
4	chr2:55331200-55339000	Weak transcription	Dnd41	blood
5	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55333200-55338800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:55334400-55340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:55334800-55339400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr2:55335000-55339000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:55335200-55339000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:55335400-55341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr2:55336600-55340000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:55337000-55338800	Weak transcription	Fetal Lung	lung
14	chr2:55337000-55339000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:55337000-55339200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:55337000-55339400	Weak transcription	Fetal Brain Female	brain
17	chr2:55337000-55340000	Weak transcription	Fetal Kidney	kidney
18	chr2:55337200-55341000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:55337400-55342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:55337400-55342800	Weak transcription	HMEC	breast
22	chr2:55337800-55339000	Weak transcription	Fetal Intestine Small	intestine
23	chr2:55338200-55339000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:55338200-55339200	Enhancers	NHLF	lung
25	chr2:55338200-55339600	Enhancers	Colon Smooth Muscle	Colon
26	chr2:55338200-55341200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:55338400-55338800	Flanking Active TSS	Fetal Heart	heart
28	chr2:55338400-55339000	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:55338400-55339400	Enhancers	H9 Cell Line	embryonic stem cell
30	chr2:55338400-55339600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr2:55338400-55339600	Enhancers	Hela-S3	cervix
32	chr2:55338400-55339800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr2:55338400-55339800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:55338400-55340200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:55338400-55340200	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr2:55338400-55340400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:55338400-55340600	Enhancers	HUVEC	blood vessel
38	chr2:55338400-55340800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:55338400-55341000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:55338400-55341200	Enhancers	Stomach Mucosa	stomach
41	chr2:55338400-55343400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:55338400-55343400	Enhancers	Primary hematopoietic stem cells	blood
43	chr2:55338600-55338800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr2:55338600-55338800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr2:55338600-55339000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:55338600-55339000	Transcr. at gene 5' and 3'	HSMM	muscle
47	chr2:55338600-55339200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:55338600-55339400	Enhancers	H1 Cell Line	embryonic stem cell
49	chr2:55338600-55339400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr2:55338600-55339400	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links