Variant report

Variant	rs12638158
Chromosome Location	chr3:142306165-142306166
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142305398..142306280-chr3:142399277..142399935,3	MCF-7	breast:
2	chr3:142297092..142299718-chr3:142303138..142306954,3	MCF-7	breast:
3	chr3:142304116..142308988-chr3:142313771..142316581,4	MCF-7	breast:
4	chr3:142304999..142307775-chr3:142720336..142721986,2	MCF-7	breast:
5	chr3:142304087..142306838-chr3:142309222..142312026,2	K562	blood:
6	chr3:142305508..142306307-chr3:142712573..142713450,4	K562	blood:
7	chr3:106647215..106647782-chr3:142305386..142306279,2	MCF-7	breast:
8	chr3:142305742..142306267-chr3:142314638..142315336,2	MCF-7	breast:
9	chr3:142305364..142306466-chr3:142399184..142400223,7	MCF-7	breast:
10	chr3:142305747..142306744-chr3:142547578..142548165,3	MCF-7	breast:
11	chr3:142305390..142308830-chr3:142313114..142316758,5	MCF-7	breast:
12	chr3:142305389..142306193-chr3:142623757..142624589,2	K562	blood:
13	chr3:142296095..142299105-chr3:142305280..142307506,3	MCF-7	breast:
14	chr3:142305688..142306265-chr3:142712595..142713344,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000120756	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000252745	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10935463	0.80[EUR][1000 genomes]
rs1129391	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11708470	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715514	0.82[EUR][1000 genomes]
rs11718899	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11916455	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11923612	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12629001	0.84[EUR][1000 genomes]
rs12629713	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12634255	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639363	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13063075	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065800	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066441	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13068397	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13070239	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072346	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13072355	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13075259	0.80[EUR][1000 genomes]
rs13085247	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085261	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092234	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092593	0.85[EUR][1000 genomes]
rs13093304	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13099184	0.80[EUR][1000 genomes]
rs2227929	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227931	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3923464	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4256152	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4558780	0.83[EUR][1000 genomes]
rs4582075	0.83[EUR][1000 genomes]
rs57299906	0.86[ASN][1000 genomes]
rs6440085	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6776402	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7432464	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7636909	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7641914	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' 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	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142298200-142314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:142298600-142314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:142305400-142306200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:142305600-142306200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:142305600-142306200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:142305600-142306200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:142305600-142306200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:142305600-142306200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:142305600-142306200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:142305600-142306200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:142305600-142306200	Enhancers	Liver	Liver
12	chr3:142305600-142306200	Enhancers	A549	lung
13	chr3:142305600-142306200	Enhancers	Hela-S3	cervix
14	chr3:142305600-142306200	Enhancers	HMEC	breast
15	chr3:142305600-142306200	Enhancers	HSMM	muscle
16	chr3:142305600-142306200	Enhancers	HSMMtube	muscle
17	chr3:142305600-142306200	Enhancers	NHDF-Ad	bronchial
18	chr3:142305600-142306200	Enhancers	NHEK	skin
19	chr3:142305600-142306200	Enhancers	Osteobl	bone
20	chr3:142305600-142306400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:142306000-142306200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links