Variant report

Variant	rs1374159
Chromosome Location	chr2:151025302-151025303
allele	C/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	CEBPB	chr2:151025024-151025553	MCF-7	breast:	n/a	chr2:151025439-151025450
2	SIN3AK20	chr2:151024919-151025634	MCF-7	breast:	n/a	n/a
3	GATA3	chr2:151025040-151025394	SH-SY5Y	brain:	n/a	n/a
4	GATA2	chr2:151025140-151025378	SH-SY5Y	brain:	n/a	n/a
5	GATA3	chr2:151025120-151025392	T-47D	breast:	n/a	n/a
6	GATA3	chr2:151024183-151025410	MCF-7	breast:	n/a	chr2:151024348-151024356 chr2:151024349-151024356 chr2:151024332-151024341 chr2:151024347-151024359 chr2:151024348-151024358 chr2:151024349-151024356 chr2:151024349-151024356
7	GATA3	chr2:151023852-151025664	MCF-7	breast:	n/a	chr2:151024348-151024356 chr2:151024349-151024356 chr2:151024332-151024341 chr2:151025470-151025479 chr2:151024347-151024359 chr2:151024348-151024358 chr2:151024349-151024356 chr2:151024349-151024356
8	CEBPB	chr2:151025258-151025627	A549	lung:	n/a	chr2:151025439-151025450
9	GATA3	chr2:151025098-151025374	T-47D	breast:	n/a	n/a
10	GATA3	chr2:151024984-151025505	SK-N-SH	brain:	n/a	chr2:151025470-151025479
11	JUND	chr2:151023929-151025900	SK-N-SH	brain:	n/a	chr2:151025471-151025480 chr2:151025472-151025481 chr2:151025472-151025480 chr2:151025473-151025480 chr2:151024331-151024340 chr2:151024330-151024339 chr2:151025470-151025481 chr2:151024329-151024340 chr2:151024331-151024339 chr2:151025470-151025482 chr2:151024332-151024339
12	GATA3	chr2:151024895-151025632	SK-N-SH	brain:	n/a	chr2:151025470-151025479
13	TCF12	chr2:151024963-151026067	SK-N-SH	brain:	n/a	n/a
14	NR2F2	chr2:151024951-151025471	MCF-7	breast:	n/a	n/a
15	GATA3	chr2:151025098-151025359	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:151019127..151021972-chr2:151024346..151026624,2	K562	blood:
2	chr2:151024105..151026870-chr2:151120233..151122729,2	MCF-7	breast:
3	chr2:151020603..151025476-chr2:151341674..151344465,7	MCF-7	breast:
4	chr2:151022947..151025702-chr2:151341739..151344961,4	MCF-7	breast:
5	chr2:151025085..151027146-chr2:151027265..151029673,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230645	TF binding region
ENSG00000115963	Chromatin interaction
ENSG00000230645	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10178850	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10180319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157219	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11685263	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11687975	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693901	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618290	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13405415	0.97[ASN][1000 genomes]
rs2376607	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28871317	0.99[ASN][1000 genomes]
rs4417736	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4567956	0.99[ASN][1000 genomes]
rs4667375	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667376	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667377	0.97[ASN][1000 genomes]
rs4667379	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6708312	0.99[ASN][1000 genomes]
rs6719194	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6721152	0.99[ASN][1000 genomes]
rs6727767	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6727863	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6750791	0.99[ASN][1000 genomes]
rs7563665	0.99[ASN][1000 genomes]
rs7601392	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9287808	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs954077	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005441	chr2:150457624-151060247	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv995119	chr2:150556150-151294696	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv469524	chr2:150927500-151076920	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv834412	chr2:151014270-151116638	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv583294	chr2:151022044-151037893	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151021800-151026200	Enhancers	NH-A	brain
2	chr2:151021800-151026800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:151022200-151026000	Enhancers	HMEC	breast
4	chr2:151022200-151026400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:151022200-151026400	Enhancers	Osteobl	bone
6	chr2:151022600-151025400	Enhancers	HUVEC	blood vessel
7	chr2:151022600-151025400	Enhancers	NHEK	skin
8	chr2:151022600-151025800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:151022600-151026400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:151023200-151025400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:151023200-151026000	Weak transcription	Aorta	Aorta
12	chr2:151023200-151026000	Weak transcription	Pancreas	Pancrea
13	chr2:151023200-151026200	Enhancers	Hela-S3	cervix
14	chr2:151023400-151025400	Enhancers	K562	blood
15	chr2:151023400-151026000	Enhancers	Liver	Liver
16	chr2:151023600-151025400	Weak transcription	Adipose Nuclei	Adipose
17	chr2:151024000-151025600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr2:151024000-151026400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:151024000-151026400	Enhancers	NHDF-Ad	bronchial
20	chr2:151024000-151026800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:151024200-151025400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:151024200-151025400	Enhancers	HSMM	muscle
23	chr2:151024200-151026000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:151024200-151026000	Enhancers	NHLF	lung
25	chr2:151024200-151026200	Enhancers	Stomach Mucosa	stomach
26	chr2:151024200-151026400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:151024800-151026000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:151024800-151026400	Enhancers	A549	lung
29	chr2:151025000-151026000	Weak transcription	Dnd41	blood
30	chr2:151025200-151025400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr2:151025200-151025400	Enhancers	Stomach Smooth Muscle	stomach
32	chr2:151025200-151025600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr2:151025200-151026600	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links