Variant report

Variant	rs2241975
Chromosome Location	chr2:113984503-113984504
allele	A/G
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	chr2:113983013..113984516-chr2:113998378..114000911,2	MCF-7	breast:
2	chr2:113983664..113985916-chr2:113988389..113990804,2	MCF-7	breast:
3	chr2:113983331..113985876-chr2:113990294..113993785,4	K562	blood:
4	chr2:113983505..113988046-chr2:113991447..113994622,4	MCF-7	breast:
5	chr2:113982222..113985690-chr2:113985752..113988361,3	MCF-7	breast:
6	chr2:113967235..113968789-chr2:113984371..113986823,2	MCF-7	breast:
7	chr2:113968640..113971575-chr2:113983814..113986609,4	MCF-7	breast:
8	chr2:113982814..113984707-chr2:113996972..113999644,2	K562	blood:
9	chr2:113978488..113981632-chr2:113983864..113986982,3	K562	blood:
10	chr2:113956459..113959352-chr2:113984317..113985947,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258395	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1478	0.81[CHB][hapmap]
rs17043176	0.84[ASW][hapmap]
rs3748915	0.82[AMR][1000 genomes]
rs3762498	0.80[AMR][1000 genomes]
rs56865224	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2241975	LOC654433	cis	brain	BrainEAC
rs2241975	LOC654433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113977400-113985600	Weak transcription	Gastric	stomach
2	chr2:113978000-113986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:113978000-113987600	Weak transcription	Esophagus	oesophagus
4	chr2:113978200-113987200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:113978200-113991800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:113978600-113984600	Genic enhancers	Fetal Kidney	kidney
7	chr2:113978800-113986200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:113980200-113991600	Weak transcription	Spleen	Spleen
9	chr2:113982600-113984600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:113982600-113984800	Enhancers	HepG2	liver
11	chr2:113982600-113987000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:113982600-113992600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:113982800-113990600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:113983200-113985600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:113983400-113984600	Enhancers	A549	lung
16	chr2:113983400-113987800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:113983400-113989000	Weak transcription	Stomach Mucosa	stomach
18	chr2:113983400-113989200	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:113983400-113991600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:113983800-113984600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:113983800-113984800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:113983800-113989800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:113983800-113991800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:113984000-113985000	Weak transcription	NH-A	brain
25	chr2:113984000-113985200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:113984000-113985800	Weak transcription	Fetal Brain Female	brain
27	chr2:113984000-113986600	Weak transcription	Fetal Intestine Small	intestine
28	chr2:113984000-113987400	Weak transcription	Pancreas	Pancrea
29	chr2:113984000-113987800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:113984000-113988400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:113984000-113990000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:113984000-113998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:113984200-113985000	Enhancers	Lung	lung
34	chr2:113984200-113985800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:113984200-113986000	Weak transcription	Fetal Intestine Large	intestine
36	chr2:113984200-113987200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:113984200-113988000	Weak transcription	Fetal Lung	lung
38	chr2:113984200-113989600	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:113984400-113985200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:113984400-113985800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:113984400-113990200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links