Variant report

Variant	rs246828
Chromosome Location	chr7:12982479-12982480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:12982252..12985209-chr7:12989086..12991470,2	MCF-7	breast:
2	chr7:12980961..12983258-chr7:13154370..13156023,2	MCF-7	breast:
3	chr7:12725676..12727718-chr7:12981615..12985353,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10254523	0.92[ASN][1000 genomes]
rs10479912	0.92[ASN][1000 genomes]
rs11765383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13236466	0.80[ASN][1000 genomes]
rs2024402	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs246826	1.00[ASN][1000 genomes]
rs28478673	0.94[ASN][1000 genomes]
rs34044	0.96[ASN][1000 genomes]
rs34048	0.99[ASN][1000 genomes]
rs34049	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34055	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34061	0.81[ASN][1000 genomes]
rs34066	0.93[ASN][1000 genomes]
rs34067	0.92[ASN][1000 genomes]
rs34068	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34073	0.83[AMR][1000 genomes]
rs34076	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34077	0.90[JPT][hapmap]
rs34078	0.82[ASN][1000 genomes]
rs4719343	1.00[ASW][hapmap];0.82[MEX][hapmap]
rs4721165	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58455143	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6969615	0.89[ASN][1000 genomes]
rs73301278	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73301284	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1020568	chr7:12802640-13183737	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv464384	chr7:12907178-13077065	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv606238	chr7:12907178-13077065	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1029771	chr7:12927648-13153855	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv538736	chr7:12927648-13153855	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1026624	chr7:12963907-13123408	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv981786	chr7:12968068-12991292	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv887642	chr7:12973609-13067198	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12979800-12991000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:12980400-12983800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:12980600-12984000	Enhancers	NHEK	skin
4	chr7:12980800-12983200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:12981200-12982800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr7:12981400-12983600	Enhancers	Fetal Intestine Large	intestine
7	chr7:12981400-12983800	Enhancers	Fetal Intestine Small	intestine
8	chr7:12981600-12983800	Enhancers	HMEC	breast
9	chr7:12981800-12982800	Enhancers	Stomach Mucosa	stomach
10	chr7:12981800-12982800	Flanking Active TSS	HepG2	liver
11	chr7:12981800-12983000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr7:12981800-12991000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:12982000-12982600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:12982000-12982600	Enhancers	Colon Smooth Muscle	Colon
15	chr7:12982000-12982600	Enhancers	Fetal Kidney	kidney
16	chr7:12982000-12982600	Enhancers	Fetal Lung	lung
17	chr7:12982000-12982600	Enhancers	Rectal Smooth Muscle	rectum
18	chr7:12982000-12982600	Enhancers	Osteobl	bone
19	chr7:12982200-12982600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr7:12982200-12982600	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr7:12982200-12982800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr7:12982200-12983800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:12982400-12982600	Enhancers	Liver	Liver
24	chr7:12982400-12982600	Flanking Active TSS	A549	lung
25	chr7:12982400-12983400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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