Variant report

Variant	rs2341059
Chromosome Location	chr2:151478268-151478269
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	TCF7L2	chr2:151478248-151478840	Hela-S3	cervix:	n/a	n/a
2	KAP1	chr2:151478226-151478836	HEK293	kidney:	n/a	n/a
3	NFIC	chr2:151478211-151478834	SK-N-SH	brain:	n/a	chr2:151478523-151478539
4	STAT3	chr2:151478232-151478808	MCF10A-Er-Src	breast:	n/a	n/a
5	NFIC	chr2:151477972-151478939	SK-N-SH	brain:	n/a	chr2:151478523-151478539
6	EP300	chr2:151478121-151478835	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr2:151478092-151478901	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr2:151478060-151478981	SK-N-SH	brain:	n/a	n/a
9	STAT3	chr2:151478186-151478772	MCF10A-Er-Src	breast:	n/a	n/a
10	TEAD4	chr2:151478194-151478863	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:151478063-151478993	SK-N-SH	brain:	n/a	n/a
12	FOS	chr2:151478136-151478813	MCF10A-Er-Src	breast:	n/a	chr2:151478529-151478540
13	JUND	chr2:151478227-151478931	SK-N-SH	brain:	n/a	n/a
14	STAT3	chr2:151478143-151478748	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr2:151478188-151478770	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr2:151478224-151478601	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr2:151478246-151478789	SK-N-SH	brain:	n/a	n/a
18	TBP	chr2:151478252-151478812	Hela-S3	cervix:	n/a	n/a
19	EP300	chr2:151478210-151478717	SK-N-SH_RA	brain:	n/a	n/a
20	FOS	chr2:151478210-151478821	MCF10A-Er-Src	breast:	n/a	chr2:151478529-151478540
21	JUND	chr2:151478212-151478947	SK-N-SH	brain:	n/a	n/a
22	MYC	chr2:151478244-151478719	MCF10A-Er-Src	breast:	n/a	n/a
23	PBX3	chr2:151478211-151478912	SK-N-SH	brain:	n/a	n/a
24	MAX	chr2:151478251-151478773	SK-N-SH	brain:	n/a	n/a
25	GATA3	chr2:151477991-151478982	SK-N-SH	brain:	n/a	n/a
26	FOSL2	chr2:151478219-151478922	SK-N-SH	brain:	n/a	n/a
27	MYC	chr2:151478229-151478733	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:151341617..151344391-chr2:151474277..151478282,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232359	TF binding region
ENSG00000115963	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10188741	0.80[ASN][1000 genomes]
rs10432416	0.80[ASN][1000 genomes]
rs10497064	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10497067	0.80[ASN][1000 genomes]
rs10497068	0.80[ASN][1000 genomes]
rs10497069	0.97[EUR][1000 genomes]
rs10930203	0.80[ASN][1000 genomes]
rs11894862	0.80[ASN][1000 genomes]
rs11899711	0.80[ASN][1000 genomes]
rs12052383	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12473120	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12614085	0.80[ASN][1000 genomes]
rs13019271	0.80[ASN][1000 genomes]
rs16828368	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs16828372	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2247416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290815	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290817	0.85[EUR][1000 genomes]
rs2341060	0.90[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341061	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341062	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341064	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341065	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341066	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2341068	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341071	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341072	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2341073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2341074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341075	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2341078	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341082	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341083	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341084	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341085	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341086	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341087	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2341088	0.80[ASN][1000 genomes]
rs2341089	0.80[ASN][1000 genomes]
rs2341090	0.80[ASN][1000 genomes]
rs2341091	0.80[ASN][1000 genomes]
rs28617484	0.81[ASN][1000 genomes]
rs2879931	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4233665	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4233666	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4233667	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4297879	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4334493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365460	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4380232	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4408725	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4514872	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4530365	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4530366	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4600650	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4627564	0.95[EUR][1000 genomes]
rs4664150	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4664689	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4664692	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56767144	0.81[ASN][1000 genomes]
rs6710003	0.80[ASN][1000 genomes]
rs6724645	0.91[EUR][1000 genomes]
rs71338158	0.84[EUR][1000 genomes]
rs7557930	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7559963	0.89[EUR][1000 genomes]
rs7560326	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7562436	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7569499	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7593427	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7597424	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7602198	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9287861	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9287862	0.80[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
rs2341059	ARL5A	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151468200-151480000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:151470200-151480400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:151473000-151487000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:151473800-151479400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:151474000-151479600	Enhancers	NHDF-Ad	bronchial
6	chr2:151474200-151479400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:151474200-151479400	Enhancers	HMEC	breast
8	chr2:151474200-151479600	Enhancers	NH-A	brain
9	chr2:151474400-151480200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:151475600-151479400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:151476000-151479600	Enhancers	HUVEC	blood vessel
12	chr2:151476200-151479200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:151476200-151479200	Enhancers	Osteobl	bone
14	chr2:151476200-151479400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:151476200-151479400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:151476200-151479400	Enhancers	NHEK	skin
17	chr2:151476200-151479600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:151476200-151479600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:151476200-151479600	Enhancers	NHLF	lung
20	chr2:151476600-151479000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:151476600-151479000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:151476600-151479600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:151476600-151479600	Enhancers	HSMM	muscle
24	chr2:151476800-151478400	Weak transcription	Fetal Stomach	stomach
25	chr2:151476800-151478600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:151476800-151478600	Weak transcription	Left Ventricle	heart
27	chr2:151476800-151480600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:151476800-151483400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:151476800-151485200	Weak transcription	Psoas Muscle	Psoas
30	chr2:151477000-151479200	Enhancers	HSMMtube	muscle
31	chr2:151477000-151479400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:151477000-151480200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:151477200-151478400	Enhancers	Colon Smooth Muscle	Colon
34	chr2:151477400-151478800	Enhancers	Adipose Nuclei	Adipose
35	chr2:151477400-151478800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:151477400-151479200	Enhancers	Ovary	ovary
37	chr2:151477400-151479400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:151477400-151479400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:151477600-151478800	Enhancers	A549	lung
40	chr2:151477600-151479000	Enhancers	Fetal Muscle Leg	muscle
41	chr2:151477600-151479200	Enhancers	Right Atrium	heart
42	chr2:151477600-151479400	Enhancers	Fetal Lung	lung
43	chr2:151477600-151479400	Enhancers	Right Ventricle	heart
44	chr2:151477800-151478400	Weak transcription	Lung	lung
45	chr2:151477800-151478600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:151477800-151478600	Weak transcription	Aorta	Aorta
47	chr2:151477800-151479400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:151477800-151480400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:151478000-151478400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:151478000-151478400	Weak transcription	Placenta Amnion	Placenta Amnion

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