Variant report

Variant	rs28609649
Chromosome Location	chr2:54781801-54781802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr2:54780916-54782067	HEK293-T-REx	kidney:	n/a	chr2:54782058-54782067

No.	Distal block	Cell Line	Cell type
1	chr2:54780815..54783412-chr2:54784470..54788233,4	K562	blood:
2	chr2:54779914..54782319-chr2:54782662..54788670,5	MCF-7	breast:
3	chr2:54771500..54773380-chr2:54779555..54782261,2	MCF-7	breast:
4	chr2:54777010..54778863-chr2:54780329..54781851,2	MCF-7	breast:

Variant related genes	Relation type
SPTBN1	TF binding region
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10169013	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171393	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172671	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10182310	1.00[ASN][1000 genomes]
rs10188548	1.00[ASN][1000 genomes]
rs10189084	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189455	0.83[EUR][1000 genomes]
rs10191357	1.00[ASN][1000 genomes]
rs10194488	1.00[ASN][1000 genomes]
rs10195423	1.00[ASN][1000 genomes]
rs10206622	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388685	0.83[EUR][1000 genomes]
rs13391762	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13403817	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414727	1.00[ASN][1000 genomes]
rs13415413	1.00[ASN][1000 genomes]
rs13415949	1.00[ASN][1000 genomes]
rs13418525	0.83[EUR][1000 genomes]
rs13423872	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425620	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13426037	1.00[ASN][1000 genomes]
rs13427468	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13428524	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13431302	1.00[ASN][1000 genomes]
rs13431815	0.83[EUR][1000 genomes]
rs17045949	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229505	1.00[ASN][1000 genomes]
rs28496426	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660202	1.00[ASN][1000 genomes]
rs28679552	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4387841	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545404	0.83[EUR][1000 genomes]
rs6545417	1.00[ASN][1000 genomes]
rs6545426	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723740	0.83[EUR][1000 genomes]
rs6735962	1.00[ASN][1000 genomes]
rs6743995	0.83[EUR][1000 genomes]
rs6746379	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757240	0.83[EUR][1000 genomes]
rs7340250	1.00[ASN][1000 genomes]
rs7355672	0.83[EUR][1000 genomes]
rs73934326	1.00[ASN][1000 genomes]
rs7574433	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808516	1.00[ASN][1000 genomes]
rs9967676	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers 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	11 gene(s)	inside rSNPs	diseases
3	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:54773800-54782200	Weak transcription	Ovary	ovary
7	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:54774000-54782400	Weak transcription	Osteobl	bone
9	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:54775800-54782400	Weak transcription	HSMM	muscle
11	chr2:54777000-54782000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:54777200-54783600	Weak transcription	Fetal Stomach	stomach
13	chr2:54777600-54782000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:54777600-54782200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:54777600-54782800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:54777600-54783600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:54777600-54784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:54777600-54784800	Weak transcription	Aorta	Aorta
19	chr2:54777800-54782200	Weak transcription	Gastric	stomach
20	chr2:54777800-54782600	Weak transcription	Fetal Kidney	kidney
21	chr2:54777800-54784200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:54778000-54782400	Weak transcription	NHLF	lung
23	chr2:54778000-54783400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:54778000-54784200	Weak transcription	Fetal Brain Male	brain
25	chr2:54778200-54783000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:54778200-54783400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:54778600-54782400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:54778600-54782600	Weak transcription	Esophagus	oesophagus
29	chr2:54778600-54784000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:54778800-54782200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:54778800-54782200	Weak transcription	HMEC	breast
32	chr2:54778800-54782400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:54778800-54782400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:54778800-54782600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:54778800-54782600	Weak transcription	NHEK	skin
36	chr2:54778800-54782800	Weak transcription	Stomach Mucosa	stomach
37	chr2:54778800-54784000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:54778800-54784000	Weak transcription	Primary B cells from cord blood	blood
39	chr2:54779000-54783600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:54779000-54783600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:54779000-54784000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr2:54779200-54783800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:54779200-54784000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:54779200-54784000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:54779200-54784200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:54779400-54782400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:54779400-54784200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:54779400-54784200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:54779800-54782800	Enhancers	HepG2	liver
50	chr2:54779800-54784200	Enhancers	NHDF-Ad	bronchial

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