Variant report

Variant	rs12533880
Chromosome Location	chr7:12734574-12734575
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:12729761..12734600-chr7:13300705..13305061,6	K562	blood:
2	chr7:12729128..12735523-chr7:12765929..12775781,12	K562	blood:
3	chr7:12733142..12735648-chr7:12788213..12790851,2	MCF-7	breast:
4	chr7:12729298..12731295-chr7:12733837..12736086,2	MCF-7	breast:
5	chr7:12732885..12735761-chr7:12786840..12788734,2	K562	blood:
6	chr7:12732805..12735607-chr7:12848862..12851491,2	K562	blood:
7	chr7:12730040..12735403-chr7:12757431..12760673,6	K562	blood:
8	chr7:12732435..12735285-chr7:12904992..12907592,2	K562	blood:
9	chr7:12734430..12737342-chr7:13081793..13084247,2	K562	blood:

No data

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10277284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976257	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11976341	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979049	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979798	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12534728	0.94[ASN][1000 genomes]
rs2241748	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280634	0.94[ASN][1000 genomes]
rs3757442	0.93[ASN][1000 genomes]
rs6952105	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6974058	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6974240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6974323	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7797379	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv830907	chr7:12661239-12818250	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv1794967	chr7:12710385-12758624	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	n/a
7	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	esv2762652	chr7:12733802-12749636	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12729000-12734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:12730200-12739000	Weak transcription	Placenta	Placenta
3	chr7:12730200-12740200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:12730400-12734600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:12730400-12735200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:12730400-12735200	Weak transcription	Stomach Mucosa	stomach
7	chr7:12730400-12735400	Weak transcription	Fetal Intestine Small	intestine
8	chr7:12730600-12734600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:12730600-12734800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:12730600-12735400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:12730800-12735400	Weak transcription	Fetal Intestine Large	intestine
12	chr7:12730800-12735400	Weak transcription	NHEK	skin
13	chr7:12730800-12746600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:12731000-12735400	Weak transcription	HMEC	breast
15	chr7:12731200-12740400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:12732000-12735000	Weak transcription	Small Intestine	intestine
17	chr7:12732400-12735600	Weak transcription	A549	lung
18	chr7:12732800-12734600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:12732800-12735400	Weak transcription	HUVEC	blood vessel
20	chr7:12733400-12737000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:12733800-12735000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr7:12733800-12736600	Enhancers	Hela-S3	cervix
23	chr7:12734000-12734600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr7:12734000-12734800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr7:12734000-12734800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:12734400-12734800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr7:12734400-12735000	Enhancers	K562	blood
28	chr7:12734400-12735400	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links