Variant report

Variant	rs4388135
Chromosome Location	chr4:159014453-159014454
allele	G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:159013562..159016824-chr4:159081048..159085392,5	MCF-7	breast:
2	chr4:159012937..159016696-chr4:159087571..159091012,3	MCF-7	breast:
3	chr4:159013245..159018298-chr4:159091169..159093561,5	MCF-7	breast:
4	chr4:159014314..159015916-chr4:159095992..159097811,2	MCF-7	breast:
5	chr4:159014385..159016745-chr4:159041064..159043729,3	MCF-7	breast:
6	chr4:158996551..158999550-chr4:159014208..159016080,2	MCF-7	breast:
7	chr4:158912571..158916849-chr4:159013907..159018478,8	MCF-7	breast:
8	chr4:159010029..159020346-chr4:159088735..159099117,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000248429	Chromatin interaction
ENSG00000164125	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10003459	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003566	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10005547	0.86[EUR][1000 genomes]
rs10005656	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10005901	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10027000	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10049927	0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs11100149	0.86[EUR][1000 genomes]
rs12503001	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13106004	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13106234	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13126694	0.81[CHB][hapmap]
rs28477319	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28514324	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34237515	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077776	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs4362869	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4487405	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4513617	0.86[EUR][1000 genomes]
rs4574459	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4631100	0.86[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs4691452	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4691460	0.94[CHB][hapmap]
rs6536298	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6814979	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs6830475	0.94[CHB][hapmap]
rs6833295	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs6843728	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6844184	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848159	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7656059	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657303	0.88[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs7692254	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9968557	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9993747	0.86[EUR][1000 genomes]
rs9995402	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv880293	chr4:159012365-159049020	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159011800-159014600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr4:159011800-159015000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:159011800-159015400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:159011800-159015400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:159011800-159015800	Weak transcription	HSMMtube	muscle
6	chr4:159012000-159015000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:159012000-159015200	Weak transcription	Osteobl	bone
8	chr4:159012000-159015400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:159012200-159015600	Weak transcription	A549	lung
10	chr4:159014200-159014600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr4:159014200-159015000	Enhancers	Ovary	ovary
12	chr4:159014200-159015200	Enhancers	HMEC	breast
13	chr4:159014200-159015800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr4:159014200-159016800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr4:159014200-159017000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:159014400-159015400	Enhancers	NHEK	skin
17	chr4:159014400-159017200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links