Variant report

Variant	rs4241315
Chromosome Location	chr2:95687104-95687105
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	TCF7L2	chr2:95686587-95687141	MCF-7	breast:	n/a	chr2:95686993-95687007
2	GATA3	chr2:95686702-95687205	T-47D	breast:	n/a	chr2:95687031-95687040
3	TEAD4	chr2:95686016-95687198	ECC-1	luminal epithelium:	n/a	chr2:95686569-95686578
4	TCF12	chr2:95686009-95687288	ECC-1	luminal epithelium:	n/a	n/a
5	EP300	chr2:95685854-95687325	ECC-1	luminal epithelium:	n/a	chr2:95686540-95686553 chr2:95686686-95686696
6	TCF12	chr2:95685793-95687361	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr2:95685992-95687120	ECC-1	luminal epithelium:	n/a	chr2:95687022-95687031
8	GATA3	chr2:95685708-95687256	MCF-7	breast:	n/a	chr2:95687031-95687040 chr2:95685778-95685789
9	MAX	chr2:95685982-95687124	ECC-1	luminal epithelium:	n/a	chr2:95687022-95687031
10	NR3C1	chr2:95686679-95687259	ECC-1	luminal epithelium:	n/a	chr2:95687179-95687205 chr2:95687179-95687205
11	GATA3	chr2:95685903-95687278	MCF-7	breast:	n/a	chr2:95687031-95687040
12	EP300	chr2:95686466-95687307	ECC-1	luminal epithelium:	n/a	chr2:95686540-95686553 chr2:95686686-95686696
13	TEAD4	chr2:95685900-95687209	ECC-1	luminal epithelium:	n/a	chr2:95686569-95686578
14	EP300	chr2:95685967-95687175	T-47D	breast:	n/a	chr2:95686540-95686553 chr2:95686686-95686696
15	EP300	chr2:95686786-95687145	T-47D	breast:	n/a	n/a
16	NFIC	chr2:95685997-95687160	ECC-1	luminal epithelium:	n/a	n/a
17	NFIC	chr2:95685935-95687234	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:95681638..95683258-chr2:95684704..95687340,2	MCF-7	breast:
2	chr2:95686313..95689732-chr2:95706916..95710668,3	MCF-7	breast:
3	chr2:95685422..95688224-chr2:95697478..95700182,2	MCF-7	breast:
4	chr2:95686559..95688225-chr2:95785641..95788692,3	MCF-7	breast:
5	chr2:95687101..95691897-chr2:95715547..95720847,7	MCF-7	breast:
6	chr2:95686086..95687912-chr2:95714512..95716349,2	MCF-7	breast:

Variant related genes	Relation type
MAL	TF binding region
ENSG00000231062	Chromatin interaction
ENSG00000144029	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10172167	0.85[CEU][hapmap]
rs17119148	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs1875402	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2291991	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2320619	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2320620	0.94[CEU][hapmap];0.89[CHB][hapmap];0.84[EUR][1000 genomes]
rs3105098	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3105099	0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.81[MKK][hapmap];0.88[ASN][1000 genomes]
rs3105100	0.82[EUR][1000 genomes]
rs3105101	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs3105104	0.95[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3105105	0.90[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3112225	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs3112228	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3112229	0.91[GIH][hapmap];0.84[TSI][hapmap]
rs3112230	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3112982	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112983	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3112984	0.94[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3112985	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3112986	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3112987	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3112995	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs3112996	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3112997	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs3113002	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[ASN][1000 genomes]
rs4555374	0.85[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs4564804	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs4854241	0.90[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4854243	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4854244	0.81[EUR][1000 genomes]
rs6708474	0.85[CEU][hapmap]
rs6723333	0.81[EUR][1000 genomes]
rs7560571	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs7565772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7582368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7585473	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs872580	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9324212	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4241315	KCNIP3	cis	cerebellum	SCAN
rs4241315	ZNF514	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95664400-95690600	Weak transcription	Right Atrium	heart
2	chr2:95681600-95688200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:95682200-95690000	Enhancers	Brain Substantia Nigra	brain
4	chr2:95684000-95687200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr2:95684800-95690200	Enhancers	Brain Angular Gyrus	brain
6	chr2:95685000-95688200	Enhancers	Brain Anterior Caudate	brain
7	chr2:95685000-95689200	Enhancers	Brain Hippocampus Middle	brain
8	chr2:95685000-95689600	Enhancers	Brain Cingulate Gyrus	brain
9	chr2:95685000-95689800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr2:95685200-95688800	Enhancers	Placenta	Placenta
11	chr2:95685600-95687800	Weak transcription	Lung	lung
12	chr2:95686000-95688200	Enhancers	Thymus	Thymus
13	chr2:95686000-95690400	Enhancers	Primary T cells from cord blood	blood
14	chr2:95686200-95687200	Flanking Active TSS	Fetal Thymus	thymus
15	chr2:95686200-95688200	Enhancers	Esophagus	oesophagus
16	chr2:95686600-95687800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
17	chr2:95686600-95688400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:95686600-95688400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:95686600-95689200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:95686800-95687200	Weak transcription	Fetal Kidney	kidney
21	chr2:95686800-95688000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:95686800-95688000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:95687000-95687200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
24	chr2:95687000-95690400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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