Variant report

Variant	rs9842407
Chromosome Location	chr3:60758206-60758207
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11130781	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130782	0.89[ASN][1000 genomes]
rs11710207	0.89[ASN][1000 genomes]
rs12185984	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059280	0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs13065371	0.89[ASN][1000 genomes]
rs13067083	0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13098348	0.89[ASN][1000 genomes]
rs13098466	0.89[ASN][1000 genomes]
rs13098545	0.89[ASN][1000 genomes]
rs13099811	0.89[ASN][1000 genomes]
rs1569346	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2064012	1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2142294	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs2205342	0.84[ASN][1000 genomes]
rs2205343	0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2205344	0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2364293	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4974227	0.86[ASN][1000 genomes]
rs4974230	0.83[CHB][hapmap]
rs57203484	0.89[ASN][1000 genomes]
rs57595293	0.89[ASN][1000 genomes]
rs60858106	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6771383	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs6786213	0.81[ASN][1000 genomes]
rs6787897	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429680	0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs926139	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9823013	0.88[CHB][hapmap]
rs9840977	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847131	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878766	0.83[CHB][hapmap]
rs9881274	0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9882068	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv999828	chr3:60537384-60785274	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60755600-60758800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:60755600-60758800	Enhancers	Placenta	Placenta
3	chr3:60755800-60758800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:60756200-60758600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:60756200-60758800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:60756200-60759000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr3:60756200-60759400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:60756200-60759600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:60756400-60759400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:60756800-60758800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr3:60757400-60758400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:60757800-60758600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:60758000-60758400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:60758000-60758600	Enhancers	Fetal Brain Female	brain
15	chr3:60758000-60758800	Enhancers	Fetal Brain Male	brain
16	chr3:60758200-60758400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:60758200-60758800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links