Variant report

Variant	rs6671050
Chromosome Location	chr1:223854562-223854563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:223854076-223854757	MCF-7	breast:	n/a	n/a
2	GATA3	chr1:223854227-223854609	T-47D	breast:	n/a	n/a
3	GATA3	chr1:223854210-223854572	T-47D	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:223831956..223833970-chr1:223853050..223855835,2	MCF-7	breast:
2	chr1:223850712..223853354-chr1:223854192..223856571,2	MCF-7	breast:
3	chr1:223836208..223847031-chr1:223849408..223858826,22	MCF-7	breast:
4	chr1:223840282..223843675-chr1:223851675..223856291,7	MCF-7	breast:
5	chr1:223825136..223827090-chr1:223853987..223856973,2	MCF-7	breast:
6	chr1:223348196..223351831-chr1:223853498..223856683,4	MCF-7	breast:
7	chr1:223833055..223835891-chr1:223854048..223855966,2	K562	blood:
8	chr1:223853852..223855706-chr1:223946715..223948642,2	K562	blood:

No data

Variant related genes	Relation type
CAPN8	TF binding region
ENSG00000203697	Chromatin interaction
ENSG00000227002	Chromatin interaction
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10495210	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10495212	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799570	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10915972	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10916633	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1109222	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125346	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12408619	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842027	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2186009	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34089008	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653518	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653520	0.86[EUR][1000 genomes]
rs4653523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653859	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653863	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4653868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4653877	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57611697	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60773808	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61825220	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6661481	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6662068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6677146	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6687391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6687688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691383	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691396	0.90[EUR][1000 genomes]
rs6693911	0.86[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs6701150	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6704218	0.83[ASN][1000 genomes]
rs68072917	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72629690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72629691	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549550	0.90[EUR][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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv873210	chr1:223707647-223856414	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv873211	chr1:223707647-223867631	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1000199	chr1:223803545-223854859	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
7	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223851800-223857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:223853000-223854600	Enhancers	Hela-S3	cervix
3	chr1:223853000-223855800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:223853200-223854600	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr1:223853400-223855000	Weak transcription	Gastric	stomach
6	chr1:223853400-223856000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:223853400-223856600	Weak transcription	Lung	lung
8	chr1:223853400-223856800	Enhancers	HMEC	breast
9	chr1:223853400-223857000	Enhancers	Stomach Mucosa	stomach
10	chr1:223853800-223854800	Weak transcription	Placenta	Placenta
11	chr1:223853800-223855200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:223853800-223855600	Weak transcription	Pancreas	Pancrea
13	chr1:223853800-223856200	Enhancers	NHEK	skin
14	chr1:223853800-223856600	Weak transcription	Esophagus	oesophagus
15	chr1:223853800-223857000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:223853800-223858400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:223854000-223854800	Weak transcription	Colonic Mucosa	Colon
18	chr1:223854000-223855800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:223854200-223855400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links