Variant report

Variant	rs9819988
Chromosome Location	chr3:135624570-135624571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135623871..135624758-chr3:135761197..135761916,3	MCF-7	breast:
2	chr3:135622647..135625440-chr3:135628057..135630167,2	K562	blood:
3	chr3:135623817..135625087-chr3:135761175..135762123,7	MCF-7	breast:

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10048942	1.00[JPT][hapmap]
rs10512973	1.00[CHB][hapmap]
rs10512981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935175	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs13072596	0.93[ASN][1000 genomes]
rs13097946	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13098245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13322891	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13325914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13434196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356664	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1401545	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1403766	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1403767	0.85[ASN][1000 genomes]
rs1403770	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1523595	0.93[ASN][1000 genomes]
rs1523596	0.93[ASN][1000 genomes]
rs1523597	0.93[ASN][1000 genomes]
rs1568349	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568350	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16843509	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17196987	0.89[GIH][hapmap];0.93[ASN][1000 genomes]
rs17197552	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17250445	0.86[ASN][1000 genomes]
rs2204259	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570106	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28855968	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28875187	0.85[ASN][1000 genomes]
rs34311570	0.86[ASN][1000 genomes]
rs35257855	0.86[ASN][1000 genomes]
rs35722356	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073308	0.85[CEU][hapmap];0.93[ASN][1000 genomes]
rs4718	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55678980	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56308637	0.85[ASN][1000 genomes]
rs56807950	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59063369	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66544356	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67039922	0.93[ASN][1000 genomes]
rs6771224	0.93[ASN][1000 genomes]
rs6771997	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6773469	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774289	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6775778	1.00[JPT][hapmap]
rs6779603	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786769	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs6802139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803447	1.00[CHB][hapmap]
rs6807058	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6807242	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6809006	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6810223	0.93[ASN][1000 genomes]
rs7433567	0.86[CEU][hapmap]
rs7609938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621331	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7621396	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7621425	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7626676	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640153	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643661	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs870812	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs908825	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9289502	0.93[ASN][1000 genomes]
rs9289503	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9808979	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9812561	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9813082	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814505	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814557	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9819440	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9820189	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9824558	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825239	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9826806	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9829329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833470	1.00[CHB][hapmap]
rs9833699	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833799	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834104	0.93[ASN][1000 genomes]
rs9834624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9836374	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9836758	1.00[JPT][hapmap]
rs9837855	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9843725	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9844478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846137	0.86[CEU][hapmap];0.93[ASN][1000 genomes]
rs9848322	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9849088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851361	0.93[ASN][1000 genomes]
rs9853577	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9854494	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862264	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9862743	0.80[ASN][1000 genomes]
rs9862763	0.93[ASN][1000 genomes]
rs9864247	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9864514	0.93[ASN][1000 genomes]
rs9864656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864775	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9868246	0.86[CEU][hapmap];0.93[ASN][1000 genomes]
rs9870581	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9872542	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9875328	0.93[ASN][1000 genomes]
rs9875948	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9876837	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877082	0.93[ASN][1000 genomes]
rs9877722	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9880721	0.93[ASN][1000 genomes]
rs9883808	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9819988	MSL2	cis	cerebellum	SCAN
rs9819988	TMEM22	cis	cerebellum	SCAN
rs9819988	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135617000-135625600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:135617000-135626000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:135624200-135624600	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links