Variant report

Variant	rs4849084
Chromosome Location	chr2:113384747-113384748
allele	A/C
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113383684..113385667-chr2:113481537..113485469,35	K562	blood:
2	chr2:113378841..113381519-chr2:113383348..113385320,2	MCF-7	breast:
3	chr16:15187795..15188622-chr2:113384234..113385184,2	Hela-S3	cervix:
4	chr2:113383343..113387238-chr2:113388797..113391596,3	MCF-7	breast:
5	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
6	chr2:113383746..113384937-chr2:113484019..113484887,5	MCF-7	breast:
7	chr2:113380240..113386960-chr2:113401832..113406779,10	MCF-7	breast:
8	chr2:113383817..113384789-chr2:113484041..113484921,7	MCF-7	breast:
9	chr2:113380970..113385799-chr2:113479613..113484625,8	K562	blood:
10	chr2:113384015..113385213-chr2:113482175..113483476,11	MCF-7	breast:
11	chr2:113383314..113385378-chr2:113441903..113443465,2	MCF-7	breast:
12	chr2:113361529..113364107-chr2:113384618..113387242,2	K562	blood:
13	chr2:113382212..113385648-chr2:113390770..113393800,3	MCF-7	breast:
14	chr2:113383706..113386562-chr2:113417388..113419756,2	MCF-7	breast:
15	chr2:113384187..113384849-chr2:113482175..113483114,3	MCF-7	breast:
16	chr2:113361529..113363513-chr2:113383774..113386118,3	K562	blood:
17	chr2:113380843..113384962-chr2:113480402..113484110,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260735	Chromatin interaction
ENSG00000231747	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000085721	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1053652	0.83[CHB][hapmap]
rs10758	0.83[CHB][hapmap]
rs11676691	0.97[EUR][1000 genomes]
rs11677284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678996	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12476928	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12479380	0.85[CHB][hapmap]
rs13023016	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387435	0.80[CHB][hapmap]
rs35743012	0.81[EUR][1000 genomes]
rs4368335	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs4848284	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs4849079	0.80[EUR][1000 genomes]
rs4849083	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4849086	0.89[CHB][hapmap]
rs62158654	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542074	0.83[CHB][hapmap]
rs6705487	0.83[CHB][hapmap]
rs6724434	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6758898	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs908545	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4849084	LOC654433	cis	parietal	SCAN
rs4849084	LOC653596	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113372400-113388600	Weak transcription	Gastric	stomach
2	chr2:113372800-113388000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:113379800-113387600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:113380200-113387600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:113380400-113387600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:113380800-113388400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:113381400-113388400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:113381600-113386000	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:113381600-113388200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:113381600-113389600	Enhancers	Placenta	Placenta
11	chr2:113381800-113385200	Flanking Active TSS	Hela-S3	cervix
12	chr2:113382000-113385800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr2:113382400-113387600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:113383000-113385200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:113383200-113384800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:113383400-113385000	Flanking Active TSS	HMEC	breast
17	chr2:113383400-113386000	Enhancers	Fetal Thymus	thymus
18	chr2:113383400-113386200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:113383600-113385800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:113383600-113385800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr2:113383600-113385800	Enhancers	K562	blood
22	chr2:113383600-113386000	Enhancers	Primary B cells from cord blood	blood
23	chr2:113383800-113385000	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:113383800-113385800	Enhancers	Fetal Muscle Leg	muscle
25	chr2:113384000-113384800	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr2:113384000-113384800	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr2:113384000-113385000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:113384000-113385200	Flanking Active TSS	A549	lung
29	chr2:113384000-113385200	Flanking Active TSS	NH-A	brain
30	chr2:113384000-113385200	Flanking Active TSS	Osteobl	bone
31	chr2:113384000-113385600	Flanking Active TSS	HSMM	muscle
32	chr2:113384000-113385800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr2:113384000-113386000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:113384000-113386000	Enhancers	Small Intestine	intestine
35	chr2:113384000-113386000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr2:113384200-113384800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:113384200-113384800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr2:113384200-113384800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:113384200-113384800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr2:113384200-113384800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr2:113384200-113384800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr2:113384200-113384800	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr2:113384200-113384800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
44	chr2:113384200-113384800	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr2:113384200-113384800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr2:113384200-113384800	Enhancers	Lung	lung
47	chr2:113384200-113384800	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr2:113384200-113384800	Enhancers	Right Atrium	heart
49	chr2:113384200-113384800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr2:113384200-113384800	Flanking Active TSS	Stomach Smooth Muscle	stomach

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