Variant report

Variant	rs2871887
Chromosome Location	chr3:141054579-141054580
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141052203..141054827-chr3:141086733..141089265,2	K562	blood:
2	chr3:141052445..141054291-chr3:141054574..141056796,2	MCF-7	breast:
3	chr3:141052611..141055656-chr3:141065180..141068176,3	K562	blood:
4	chr3:141046937..141049134-chr3:141051333..141055060,4	K562	blood:
5	chr3:141054208..141057606-chr3:141059807..141061537,3	K562	blood:
6	chr3:141053417..141055018-chr3:141104331..141106494,2	MCF-7	breast:
7	chr3:141051493..141053638-chr3:141053830..141056565,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACPL2-2	chr3:141053584-141054644	NONHSAT092426

No data

Variant related genes	Relation type
ENSG00000177311	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10513140	1.00[LWK][hapmap]
rs13088239	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13094525	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1346408	1.00[YRI][hapmap]
rs1983233	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439999	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6778010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807533	0.99[ASN][1000 genomes]
rs72986540	0.95[ASN][1000 genomes]
rs72986545	0.98[ASN][1000 genomes]
rs7613516	1.00[YRI][hapmap]
rs9838625	0.83[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141046200-141055800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:141046400-141055800	Genic enhancers	Fetal Intestine Small	intestine
3	chr3:141047000-141055800	Genic enhancers	Fetal Intestine Large	intestine
4	chr3:141049000-141056600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:141049200-141055000	Enhancers	GM12878-XiMat	blood
6	chr3:141049200-141057000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:141049400-141056800	Enhancers	NHLF	lung
8	chr3:141050600-141057000	Enhancers	NHDF-Ad	bronchial
9	chr3:141050800-141055800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:141051000-141055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:141051000-141055600	Weak transcription	NHEK	skin
12	chr3:141051200-141054800	Weak transcription	HMEC	breast
13	chr3:141051200-141055600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:141052200-141055400	Weak transcription	HUVEC	blood vessel
15	chr3:141052200-141056400	Enhancers	A549	lung
16	chr3:141052400-141056000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:141052400-141056000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:141052600-141055600	Weak transcription	Small Intestine	intestine
19	chr3:141052600-141056000	Weak transcription	Colonic Mucosa	Colon
20	chr3:141052600-141056000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:141052600-141056600	Enhancers	Osteobl	bone
22	chr3:141053000-141054800	Weak transcription	HSMM	muscle
23	chr3:141053000-141055000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:141053000-141055800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:141053000-141055800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:141053200-141055800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:141053400-141054600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:141053400-141054800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr3:141053400-141054800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr3:141053400-141055000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:141053400-141055000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:141053400-141056600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:141053800-141056800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:141053800-141058200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:141054000-141056600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:141054200-141054800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:141054200-141056000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:141054200-141056600	Enhancers	Hela-S3	cervix
39	chr3:141054200-141057000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:141054400-141054600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:141054400-141054600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:141054400-141054600	Enhancers	Brain Hippocampus Middle	brain
43	chr3:141054400-141056000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:141054400-141056000	Enhancers	NH-A	brain
45	chr3:141054400-141056600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:141054400-141056600	Enhancers	K562	blood
47	chr3:141054400-141056800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:141054400-141056800	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links