Variant report

Variant	rs2121721
Chromosome Location	chr3:160685788-160685789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160685063..160687568-chr3:161087715..161090731,3	MCF-7	breast:
2	chr3:160683839..160685876-chr3:160685916..160688095,2	K562	blood:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10513558	0.85[JPT][hapmap]
rs10513560	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10936216	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709802	0.82[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs12494673	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs12690576	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs12696110	0.85[JPT][hapmap]
rs1374787	0.84[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1447608	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];0.96[ASN][1000 genomes]
rs1447609	0.95[EUR][1000 genomes]
rs1530636	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1562465	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1580253	0.88[EUR][1000 genomes]
rs1580254	0.80[TSI][hapmap]
rs1868104	0.88[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs1868106	0.85[JPT][hapmap]
rs1868108	0.84[CEU][hapmap]
rs1868109	0.83[CEU][hapmap];0.81[CHD][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2028988	0.88[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2376476	0.82[EUR][1000 genomes]
rs2376477	0.83[EUR][1000 genomes]
rs2889391	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34462546	0.94[EUR][1000 genomes]
rs4679667	0.85[JPT][hapmap]
rs4679928	0.81[EUR][1000 genomes]
rs6441345	0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441346	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6763532	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6770180	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6770488	0.85[JPT][hapmap]
rs6774203	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs6797498	0.83[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6808386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs733948	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs7610732	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs7611005	0.81[EUR][1000 genomes]
rs7613316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7616249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7619552	0.86[ASN][1000 genomes]
rs7626904	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7626985	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7629001	0.85[ASN][1000 genomes]
rs7635796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7640874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7644586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653744	0.86[ASN][1000 genomes]
rs778655	0.85[JPT][hapmap]
rs898682	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs956447	0.84[CEU][hapmap]
rs9813700	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9839984	0.80[TSI][hapmap]
rs9840600	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs9846254	0.92[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs9857743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858335	0.80[TSI][hapmap]
rs9860182	0.96[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs9881807	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	esv3462791	chr3:160680085-160686174	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3462792	chr3:160680137-160686148	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3462790	chr3:160680198-160686110	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3462793	chr3:160680198-160686110	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv16422	chr3:160680271-160685991	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv592130	chr3:160681614-160685894	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv592131	chr3:160682296-160685788	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv592132	chr3:160682296-160685894	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv592134	chr3:160682500-160685894	Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv592135	chr3:160682500-160689164	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2121721	PPM1L	cis	cerebellum	SCAN
rs2121721	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs2121721	C3orf57	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160667400-160696000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:160670200-160686600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:160670400-160686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:160678400-160697600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:160679000-160686600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:160681000-160686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:160682400-160686600	Weak transcription	Left Ventricle	heart
9	chr3:160683800-160687000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:160684600-160689200	Weak transcription	Dnd41	blood
11	chr3:160685200-160686800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:160685400-160686800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:160685400-160687000	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links