Variant report

Variant	rs2000317
Chromosome Location	chr1:223855220-223855221
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:223855218-223855565	K562	blood:	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
ENSG00000162909	Chromatin interaction
ENSG00000203697	Chromatin interaction
ENSG00000227002	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10753427	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10799364	1.00[AMR][1000 genomes]
rs10915854	1.00[AMR][1000 genomes]
rs10916015	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12021978	0.89[ASN][1000 genomes]
rs12030569	0.95[ASN][1000 genomes]
rs12032635	0.93[ASN][1000 genomes]
rs12034086	0.95[ASN][1000 genomes]
rs12037022	0.93[ASN][1000 genomes]
rs12042187	0.95[ASN][1000 genomes]
rs12042337	0.95[ASN][1000 genomes]
rs1222144	1.00[AMR][1000 genomes]
rs1361915	1.00[AMR][1000 genomes]
rs1539703	1.00[AMR][1000 genomes]
rs16842210	1.00[AMR][1000 genomes]
rs16842251	1.00[AMR][1000 genomes]
rs1857549	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1892071	1.00[AMR][1000 genomes]
rs1892074	1.00[AMR][1000 genomes]
rs1892075	1.00[AMR][1000 genomes]
rs1977898	1.00[AMR][1000 genomes]
rs2096343	1.00[AMR][1000 genomes]
rs2154115	1.00[AMR][1000 genomes]
rs2186005	1.00[AMR][1000 genomes]
rs2404288	1.00[AMR][1000 genomes]
rs25655	1.00[AMR][1000 genomes]
rs28370086	1.00[AMR][1000 genomes]
rs28370105	1.00[AMR][1000 genomes]
rs28370108	1.00[AMR][1000 genomes]
rs4653792	1.00[AMR][1000 genomes]
rs4653866	1.00[AMR][1000 genomes]
rs4653869	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6422641	1.00[AMR][1000 genomes]
rs6688648	1.00[AMR][1000 genomes]
rs7538151	1.00[AMR][1000 genomes]
rs7554290	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
6	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
7	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:16 , 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	chr1:223853000-223855800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:223853400-223856000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:223853400-223856600	Weak transcription	Lung	lung
5	chr1:223853400-223856800	Enhancers	HMEC	breast
6	chr1:223853400-223857000	Enhancers	Stomach Mucosa	stomach
7	chr1:223853800-223855600	Weak transcription	Pancreas	Pancrea
8	chr1:223853800-223856200	Enhancers	NHEK	skin
9	chr1:223853800-223856600	Weak transcription	Esophagus	oesophagus
10	chr1:223853800-223857000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:223853800-223858400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:223854000-223855800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:223854200-223855400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:223854600-223855600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:223854800-223857000	Enhancers	Colonic Mucosa	Colon
16	chr1:223855000-223857000	Enhancers	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links