Variant report

Variant	rs28702871
Chromosome Location	chr2:46936265-46936266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46933593..46936563-chr2:46968141..46970927,2	K562	blood:
2	chr2:46924668..46928828-chr2:46932943..46938478,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10164807	1.00[AMR][1000 genomes]
rs10172110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10189994	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10190001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10190187	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11125088	1.00[AMR][1000 genomes]
rs13399713	1.00[AMR][1000 genomes]
rs13402553	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418951	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41409850	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41483445	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6711782	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6714964	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6716072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6759784	1.00[AMR][1000 genomes]
rs6760403	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73926574	1.00[AMR][1000 genomes]
rs73926585	1.00[AMR][1000 genomes]
rs7566758	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7573534	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9807932	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9808073	1.00[AMR][1000 genomes]
rs9808427	1.00[AMR][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	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46927800-46940000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:46928000-46943600	Weak transcription	Thymus	Thymus
3	chr2:46928600-46944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:46928800-46938600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:46928800-46946200	Weak transcription	NHEK	skin
6	chr2:46929000-46940200	Weak transcription	Fetal Stomach	stomach
7	chr2:46930000-46938400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:46930400-46936400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:46931200-46938800	Weak transcription	Primary B cells from cord blood	blood
10	chr2:46931800-46936800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:46932000-46936400	Enhancers	Adipose Nuclei	Adipose
12	chr2:46932400-46936800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:46932400-46937000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr2:46932400-46938800	Weak transcription	Primary T cells from cord blood	blood
15	chr2:46932600-46944200	Weak transcription	Aorta	Aorta
16	chr2:46933000-46936400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:46933000-46943600	Weak transcription	Left Ventricle	heart
18	chr2:46933200-46936800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:46933400-46936400	Weak transcription	Fetal Lung	lung
20	chr2:46933800-46936600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr2:46933800-46936600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:46933800-46936800	Enhancers	A549	lung
23	chr2:46933800-46936800	Enhancers	HepG2	liver
24	chr2:46933800-46937000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:46934000-46937000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:46934000-46944200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:46934000-46947800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:46934200-46936600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:46934400-46943600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:46934600-46936400	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:46934600-46937200	Enhancers	Osteobl	bone
32	chr2:46934600-46938000	Enhancers	NHDF-Ad	bronchial
33	chr2:46934600-46946400	Weak transcription	HSMM	muscle
34	chr2:46935200-46936400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:46935200-46936400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:46935200-46936800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr2:46935200-46937000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:46935200-46944000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:46935400-46936400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:46935800-46936400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:46935800-46936400	Enhancers	Pancreas	Pancrea
42	chr2:46935800-46936400	Enhancers	Psoas Muscle	Psoas
43	chr2:46935800-46936400	Enhancers	Right Atrium	heart
44	chr2:46935800-46936600	Enhancers	H9 Cell Line	embryonic stem cell
45	chr2:46935800-46937000	Enhancers	Ovary	ovary
46	chr2:46935800-46937200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:46935800-46938000	Weak transcription	NHLF	lung
48	chr2:46936000-46936400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:46936000-46936400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:46936000-46938600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links