Variant report

Variant	rs11729600
Chromosome Location	chr4:9764686-9764687
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:91815162..91820044-chr4:9763391..9768700,25	MCF-7	breast:
2	chr1:149221736..149225365-chr4:9763717..9766826,4	MCF-7	breast:
3	chr4:9764417..9765133-chr4:10016121..10017439,5	MCF-7	breast:
4	chr4:9764445..9765327-chr4:10020033..10020988,3	K562	blood:
5	chr4:9764437..9765430-chr4:10020023..10020916,6	MCF-7	breast:
6	chr4:9764370..9765339-chr4:10015197..10016013,4	MCF-7	breast:
7	chr4:9763456..9766236-chr4:10014004..10016919,3	K562	blood:
8	chr2:91816303..91817383-chr4:9764391..9765414,6	MCF-7	breast:
9	chr2:91816443..91817305-chr4:9764390..9765414,6	MCF-7	breast:
10	chr4:9764428..9765300-chr4:10016550..10017565,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction
ENSG00000109667	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10939504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939507	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939514	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723334	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11733815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734890	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501256	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1519094	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1519095	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1533615	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1818670	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1850735	0.85[AFR][1000 genomes]
rs1850737	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1850739	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[YRI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1878275	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280208	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2867388	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3973946	0.85[ASN][1000 genomes]
rs4299578	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4697896	1.00[YRI][hapmap]
rs6448982	0.87[EUR][1000 genomes]
rs6449000	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6449027	1.00[YRI][hapmap]
rs6449028	1.00[YRI][hapmap]
rs6833148	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6834270	0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6834512	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6834697	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6841978	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6858644	0.87[EUR][1000 genomes]
rs7657127	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7661082	0.93[EUR][1000 genomes]
rs7664304	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664572	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7668469	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7685974	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9685502	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
2	esv2754610	chr4:9372303-9804524	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
4	nsv1012865	chr4:9429299-9794181	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1001143	chr4:9435322-9794181	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1012621	chr4:9456977-9802366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1012634	chr4:9461218-9802366	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
8	nsv998043	chr4:9496282-9830208	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
9	nsv878667	chr4:9543673-9903121	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv878669	chr4:9551094-9794724	Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv964031	chr4:9629449-9764955	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv999102	chr4:9633247-9794181	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1014216	chr4:9713612-10223836	Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	nsv1010249	chr4:9716101-10086188	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9755800-9766200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:9760400-9766200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:9760600-9765000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:9763600-9767600	Weak transcription	Right Atrium	heart
5	chr4:9764400-9764800	Enhancers	Fetal Intestine Small	intestine
6	chr4:9764400-9765200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:9764600-9765000	Enhancers	Fetal Intestine Large	intestine
8	chr4:9764600-9765200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr4:9764600-9765200	Enhancers	Fetal Stomach	stomach
10	chr4:9764600-9765200	Enhancers	Fetal Thymus	thymus
11	chr4:9764600-9765200	Enhancers	HepG2	liver
12	chr4:9764600-9765400	Enhancers	Fetal Muscle Leg	muscle

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