Variant report

Variant	rs11676530
Chromosome Location	chr2:151467243-151467244
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	PAX5	chr2:151467151-151467561	GM12892	blood:	n/a	chr2:151467370-151467387 chr2:151467368-151467386 chr2:151467377-151467386
3	RAD21	chr2:151467151-151467609	H1-hESC	embryonic stem cell:	n/a	chr2:151467389-151467408
4	CEBPB	chr2:151467196-151467563	Hela-S3	cervix:	n/a	n/a
5	RAD21	chr2:151467198-151467551	GM12878	blood:	n/a	chr2:151467389-151467408
6	CTCF	chr2:151467043-151467647	HCT-116	colon:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
7	RAD21	chr2:151467164-151467634	SK-N-SH_RA	brain:	n/a	chr2:151467389-151467408
8	SMC3	chr2:151467222-151467552	HepG2	liver:	n/a	n/a
9	RAD21	chr2:151466361-151467686	IMR90	lung:	n/a	chr2:151467389-151467408
10	RAD21	chr2:151467087-151467673	A549	lung:	n/a	chr2:151467389-151467408
11	RAD21	chr2:151467043-151467581	HCT-116	colon:	n/a	chr2:151467389-151467408
12	STAT3	chr2:151467139-151467477	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr2:151466956-151467783	SK-N-SH	brain:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
14	CTCF	chr2:151467220-151467370	A549	lung:	n/a	n/a
15	PAX5	chr2:151467148-151467567	GM12878	blood:	n/a	chr2:151467370-151467387 chr2:151467368-151467386 chr2:151467377-151467386
16	CTCF	chr2:151467171-151467588	H1-hESC	embryonic stem cell:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
17	SMC3	chr2:151467192-151467570	GM12878	blood:	n/a	n/a
18	RAD21	chr2:151467120-151467544	SK-N-SH_RA	brain:	n/a	chr2:151467389-151467408
19	CTCF	chr2:151467196-151467560	A549	lung:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
20	RAD21	chr2:151466953-151467755	A549	lung:	n/a	chr2:151467389-151467408
21	TCF12	chr2:151466111-151467677	SK-N-SH	brain:	n/a	n/a
22	CEBPB	chr2:151466850-151467508	A549	lung:	n/a	n/a
23	CTCF	chr2:151467240-151467390	HRE	kidney:	n/a	n/a
24	PAX5	chr2:151467182-151467588	GM12878	blood:	n/a	chr2:151467370-151467387 chr2:151467368-151467386 chr2:151467377-151467386
25	RAD21	chr2:151467119-151467637	ECC-1	luminal epithelium:	n/a	chr2:151467389-151467408
26	RAD21	chr2:151467161-151467612	H1-hESC	embryonic stem cell:	n/a	chr2:151467389-151467408
27	RAD21	chr2:151467035-151467636	H1-hESC	embryonic stem cell:	n/a	chr2:151467389-151467408
28	RFX5	chr2:151467213-151467561	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr2:151466342-151467958	A549	lung:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
30	PBX3	chr2:151467140-151467729	SK-N-SH	brain:	n/a	n/a
31	STAT3	chr2:151467217-151467599	Hela-S3	cervix:	n/a	n/a
32	SMC3	chr2:151466919-151467637	Hela-S3	cervix:	n/a	n/a
33	MAX	chr2:151467165-151467520	Hela-S3	cervix:	n/a	n/a
34	MXI1	chr2:151466194-151467708	IMR90	lung:	n/a	n/a
35	E2F4	chr2:151467204-151467501	MCF10A-Er-Src	breast:	n/a	n/a
36	MYC	chr2:151467156-151467556	MCF10A-Er-Src	breast:	n/a	n/a
37	CTCF	chr2:151467232-151467593	H1-hESC	embryonic stem cell:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
38	CTCF	chr2:151467099-151467631	MCF-7	breast:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
39	PAX5	chr2:151467197-151467527	GM12878	blood:	n/a	chr2:151467370-151467387 chr2:151467368-151467386 chr2:151467377-151467386
40	RAD21	chr2:151467188-151467555	HepG2	liver:	n/a	chr2:151467389-151467408
41	RAD21	chr2:151467191-151467609	A549	lung:	n/a	chr2:151467389-151467408
42	BRCA1	chr2:151467130-151467518	Hela-S3	cervix:	n/a	n/a
43	PBX3	chr2:151467139-151467661	SK-N-SH	brain:	n/a	n/a
44	CTCF	chr2:151467220-151467370	WI-38	lung:	n/a	n/a
45	CTCF	chr2:151467194-151467607	HCT-116	colon:	n/a	chr2:151467393-151467406 chr2:151467391-151467409 chr2:151467392-151467408
46	PAX5	chr2:151467041-151467581	GM12878	blood:	n/a	chr2:151467370-151467387 chr2:151467368-151467386 chr2:151467377-151467386
47	RAD21	chr2:151467126-151467577	HepG2	liver:	n/a	chr2:151467389-151467408
48	RAD21	chr2:151467204-151467571	HepG2	liver:	n/a	chr2:151467389-151467408
49	RAD21	chr2:151467215-151467473	GM12878	blood:	n/a	chr2:151467389-151467408
50	JUND	chr2:151467187-151467579	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:151383148..151383912-chr2:151466904..151467549,2	MCF-7	breast:
2	chr2:151466968..151467825-chr2:151907836..151908382,2	MCF-7	breast:
3	chr2:151338744..151345527-chr2:151464975..151472294,14	MCF-7	breast:
4	chr2:150453295..150455757-chr2:151465590..151467443,2	MCF-7	breast:
5	chr2:151343940..151344674-chr2:151466969..151467781,2	MCF-7	breast:
6	chr2:151466148..151468883-chr2:151471106..151473302,2	MCF-7	breast:
7	chr2:151340761..151344289-chr2:151463016..151468103,7	MCF-7	breast:
8	chr2:151343903..151344710-chr2:151466880..151467605,2	MCF-7	breast:

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

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17197737	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879878	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864164	1.00[ASN][1000 genomes]
rs72865909	1.00[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11676530	NOS1AP	trans	parietal	SCAN

Chromatin state (count:33 , 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	chr2:151463000-151467400	Enhancers	HSMMtube	muscle
5	chr2:151463000-151467600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:151463000-151467600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:151463400-151467600	Enhancers	NHLF	lung
8	chr2:151464400-151476200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:151465600-151467400	Enhancers	A549	lung
10	chr2:151466000-151467400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:151466200-151467400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:151466200-151467400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:151466200-151467400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:151466200-151469600	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:151466400-151467400	Enhancers	Adipose Nuclei	Adipose
16	chr2:151466400-151467400	Enhancers	Liver	Liver
17	chr2:151466400-151467400	Enhancers	Dnd41	blood
18	chr2:151466600-151467400	Enhancers	Osteobl	bone
19	chr2:151466600-151469600	Weak transcription	Right Atrium	heart
20	chr2:151466800-151467400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:151466800-151467400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:151466800-151467800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:151466800-151469200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:151467000-151467400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr2:151467000-151467400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr2:151467000-151467400	Enhancers	NHDF-Ad	bronchial
27	chr2:151467000-151467400	Enhancers	NHEK	skin
28	chr2:151467000-151469200	Weak transcription	Fetal Lung	lung
29	chr2:151467000-151469400	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:151467000-151475600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:151467200-151467400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:151467200-151467400	Enhancers	HMEC	breast
33	chr2:151467200-151474200	Weak transcription	HSMM	muscle

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