Variant report

Variant	rs2340863
Chromosome Location	chr2:151467617-151467618
allele	A/G
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	RAD21	chr2:151467133-151467711	MCF-7	breast:	n/a	chr2:151467389-151467408
2	CTCF	chr2:151467043-151467647	HCT-116	colon:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
3	RAD21	chr2:151467164-151467634	SK-N-SH_RA	brain:	n/a	chr2:151467389-151467408
4	RAD21	chr2:151466361-151467686	IMR90	lung:	n/a	chr2:151467389-151467408
5	RAD21	chr2:151467087-151467673	A549	lung:	n/a	chr2:151467389-151467408
6	CTCF	chr2:151466956-151467783	SK-N-SH	brain:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
7	RAD21	chr2:151466953-151467755	A549	lung:	n/a	chr2:151467389-151467408
8	TCF12	chr2:151466111-151467677	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr2:151467119-151467637	ECC-1	luminal epithelium:	n/a	chr2:151467389-151467408
10	RAD21	chr2:151467035-151467636	H1-hESC	embryonic stem cell:	n/a	chr2:151467389-151467408
11	CTCF	chr2:151466342-151467958	A549	lung:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
12	PBX3	chr2:151467140-151467729	SK-N-SH	brain:	n/a	n/a
13	SMC3	chr2:151466919-151467637	Hela-S3	cervix:	n/a	n/a
14	MXI1	chr2:151466194-151467708	IMR90	lung:	n/a	n/a
15	CTCF	chr2:151467099-151467631	MCF-7	breast:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
16	PBX3	chr2:151467139-151467661	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr2:151466997-151467931	SK-N-SH	brain:	n/a	chr2:151467389-151467408
18	FOS	chr2:151467276-151467628	MCF10A-Er-Src	breast:	n/a	n/a
19	RAD21	chr2:151467001-151467670	HCT-116	colon:	n/a	chr2:151467389-151467408
20	CTCF	chr2:151467193-151467638	MCF-7	breast:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
21	TCF12	chr2:151467105-151467687	A549	lung:	n/a	n/a
22	RAD21	chr2:151467097-151467659	MCF-7	breast:	n/a	chr2:151467389-151467408
23	SMC3	chr2:151466185-151467763	SK-N-SH	brain:	n/a	n/a
24	RAD21	chr2:151467077-151467630	ECC-1	luminal epithelium:	n/a	chr2:151467389-151467408

No.	Distal block	Cell Line	Cell type
1	chr2:151466968..151467825-chr2:151907836..151908382,2	MCF-7	breast:
2	chr2:151338744..151345527-chr2:151464975..151472294,14	MCF-7	breast:
3	chr2:151343940..151344674-chr2:151466969..151467781,2	MCF-7	breast:
4	chr2:151466148..151468883-chr2:151471106..151473302,2	MCF-7	breast:
5	chr2:151340761..151344289-chr2:151463016..151468103,7	MCF-7	breast:
6	chr2:150453802..150454699-chr2:151467290..151467940,2	K562	blood:

Variant related genes	Relation type
ENSG00000224048	TF binding region
ENSG00000115963	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10202222	0.94[AFR][1000 genomes]
rs11685634	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2340860	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2340861	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2340862	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2879927	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4233661	0.80[AMR][1000 genomes]
rs4664659	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6758119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv834415	chr2:151374254-151558649	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2757836	chr2:151457277-151844210	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv2759096	chr2:151457277-151844210	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151458200-151469400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:151458600-151469400	Weak transcription	Aorta	Aorta
3	chr2:151462800-151471000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:151464400-151476200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:151466200-151469600	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:151466600-151469600	Weak transcription	Right Atrium	heart
7	chr2:151466800-151467800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:151466800-151469200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:151467000-151469200	Weak transcription	Fetal Lung	lung
10	chr2:151467000-151469400	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:151467000-151475600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:151467200-151474200	Weak transcription	HSMM	muscle
13	chr2:151467400-151469200	Weak transcription	HSMMtube	muscle
14	chr2:151467400-151469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:151467400-151469400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:151467400-151469400	Weak transcription	Adipose Nuclei	Adipose
17	chr2:151467400-151469400	Weak transcription	Liver	Liver
18	chr2:151467400-151469400	Weak transcription	NHEK	skin
19	chr2:151467400-151469600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:151467400-151470000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:151467400-151474200	Weak transcription	HMEC	breast
22	chr2:151467400-151476200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:151467400-151476200	Weak transcription	Osteobl	bone
24	chr2:151467600-151467800	Enhancers	NHDF-Ad	bronchial
25	chr2:151467600-151469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:151467600-151469200	Weak transcription	NHLF	lung
27	chr2:151467600-151469800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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