Variant report

Variant	rs10947949
Chromosome Location	chr6:12330437-12330438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12313605..12316031-chr6:12327791..12330633,2	MCF-7	breast:
2	chr6:12330412..12331925-chr6:12484463..12486151,2	MCF-7	breast:
3	chr6:12289926..12292428-chr6:12329322..12332076,4	MCF-7	breast:
4	chr6:12297751..12299644-chr6:12328218..12330903,2	MCF-7	breast:
5	chr6:12329368..12332356-chr6:12340558..12342942,2	MCF-7	breast:
6	chr6:12286691..12293887-chr6:12327157..12336724,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078401	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10947948	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11753558	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12055484	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17765653	0.80[AMR][1000 genomes]
rs4379286	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711655	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4714383	0.81[EUR][1000 genomes]
rs4714418	0.82[AMR][1000 genomes]
rs6458187	0.89[EUR][1000 genomes]
rs6458193	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6921790	0.82[ASN][1000 genomes]
rs6932390	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357346	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369262	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9381015	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9381035	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394741	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9462681	0.82[EUR][1000 genomes]
rs9462684	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 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	chr6:12324800-12331000	Weak transcription	Pancreas	Pancrea
2	chr6:12325200-12331600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:12325200-12332200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:12325400-12331000	Weak transcription	Fetal Intestine Large	intestine
5	chr6:12325400-12332000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:12327400-12334600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:12327800-12337000	Enhancers	HepG2	liver
8	chr6:12328000-12335200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:12328800-12334000	Enhancers	Stomach Mucosa	stomach
10	chr6:12328800-12334800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:12329200-12331600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:12329400-12331000	Weak transcription	Fetal Intestine Small	intestine
13	chr6:12329400-12331000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:12329400-12332200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:12329400-12334600	Weak transcription	Hela-S3	cervix
16	chr6:12329400-12335400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:12329400-12336000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:12329400-12336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:12329600-12331000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:12330000-12331000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:12330000-12331000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:12330000-12332000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:12330200-12330600	Weak transcription	HMEC	breast
24	chr6:12330200-12332200	Weak transcription	NHEK	skin
25	chr6:12330400-12330800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links