Variant report

Variant	rs342054
Chromosome Location	chr2:20650965-20650966
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:9)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
2	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
3	chr2:20549000..20550935-chr2:20649579..20652329,2	MCF-7	breast:
4	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:
5	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
6	chr2:20648875..20651258-chr7:86847173..86848866,2	MCF-7	breast:
7	chr2:20592640..20602218-chr2:20644635..20652468,15	MCF-7	breast:
8	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
9	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RHOB-1	chr2:20650297-20651580	NONHSAT069442
2	lnc-RHOB-1	chr2:20650297-20651580	FPKM1_group_15529_transcript_1
3	lnc-RHOB-1	chr2:20650311-20652994	FPKM1_group_15529_transcript_1

No data

Variant related genes	Relation type
ENSG00000118960	Chromatin interaction
ENSG00000212171	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000200397	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2602160	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs2924378	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs342055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs342056	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs342054	AC023137.2	cis	Artery Tibial	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20648600-20651000	Active TSS	Aorta	Aorta
2	chr2:20649000-20651400	Enhancers	Placenta Amnion	Placenta Amnion
3	chr2:20649000-20651600	Enhancers	Fetal Heart	heart
4	chr2:20649000-20652000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:20649000-20652200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:20649200-20651000	Flanking Active TSS	Fetal Brain Female	brain
7	chr2:20649400-20651000	Flanking Active TSS	Hela-S3	cervix
8	chr2:20649400-20651000	Enhancers	HMEC	breast
9	chr2:20649400-20651400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:20649600-20651000	Enhancers	Stomach Mucosa	stomach
11	chr2:20649600-20651000	Flanking Active TSS	HUVEC	blood vessel
12	chr2:20649600-20651400	Enhancers	Fetal Kidney	kidney
13	chr2:20649600-20651400	Enhancers	Fetal Lung	lung
14	chr2:20649600-20651600	Enhancers	HSMM	muscle
15	chr2:20649800-20651000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:20649800-20651200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:20649800-20653000	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr2:20649800-20653000	Enhancers	Placenta	Placenta
19	chr2:20650000-20651400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr2:20650000-20651400	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr2:20650200-20651000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
22	chr2:20650200-20651400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr2:20650200-20652600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:20650400-20651000	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr2:20650400-20651400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:20650400-20651400	Enhancers	NHDF-Ad	bronchial
27	chr2:20650400-20651600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:20650400-20652200	Enhancers	Fetal Muscle Leg	muscle
29	chr2:20650400-20653000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:20650400-20653200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:20650600-20651000	Weak transcription	Psoas Muscle	Psoas
32	chr2:20650600-20651000	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr2:20650600-20651000	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:20650600-20651200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:20650600-20651200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr2:20650600-20651200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:20650600-20651200	Enhancers	A549	lung
38	chr2:20650600-20651400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:20650600-20651400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:20650600-20651400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr2:20650600-20651600	Enhancers	Fetal Intestine Small	intestine
42	chr2:20650600-20651800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:20650600-20651800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:20650600-20652000	Weak transcription	Esophagus	oesophagus
45	chr2:20650600-20652000	Weak transcription	Ovary	ovary
46	chr2:20650600-20652400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:20650600-20652400	Enhancers	Osteobl	bone
48	chr2:20650600-20652600	Enhancers	Fetal Stomach	stomach
49	chr2:20650600-20652800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:20650600-20652800	Enhancers	HepG2	liver

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