Variant report

Variant	rs1229579
Chromosome Location	chr10:93849003-93849004
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:93843200..93844774-chr10:93846231..93849117,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10786029	0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10786031	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786033	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10882028	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10882042	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1099379	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11186755	1.00[YRI][hapmap]
rs1137825	1.00[YRI][hapmap]
rs1229578	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12413858	1.00[YRI][hapmap]
rs12571564	1.00[YRI][hapmap]
rs12763600	1.00[YRI][hapmap]
rs12774665	1.00[YRI][hapmap]
rs1622656	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1711849	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971471	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2676817	1.00[YRI][hapmap]
rs2676819	1.00[YRI][hapmap]
rs2676820	1.00[YRI][hapmap]
rs2676822	1.00[YRI][hapmap]
rs2767654	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2792022	1.00[YRI][hapmap]
rs2797639	1.00[YRI][hapmap]
rs3781229	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3824734	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4642988	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4933227	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4933228	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4933229	0.81[AMR][1000 genomes]
rs4933705	1.00[YRI][hapmap]
rs4933706	1.00[YRI][hapmap]
rs6583804	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs701844	0.95[ASN][1000 genomes]
rs701846	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7078559	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7087501	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7090737	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7091853	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7908721	0.81[AMR][1000 genomes]
rs7919699	0.82[ASN][1000 genomes]
rs7919840	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7920520	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs833367	1.00[YRI][hapmap]
rs833372	1.00[YRI][hapmap]
rs833384	1.00[YRI][hapmap]
rs833385	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs855698	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855699	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855702	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855703	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855704	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855706	0.83[ASN][1000 genomes]
rs855707	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855708	0.92[ASN][1000 genomes]
rs855710	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1042818	chr10:93715483-93855032	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv895893	chr10:93747260-93875264	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93836000-93853200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:93841200-93853800	Weak transcription	Pancreas	Pancrea
3	chr10:93841200-93872400	Weak transcription	Spleen	Spleen
4	chr10:93841200-93881600	Weak transcription	Esophagus	oesophagus
5	chr10:93844000-93851200	Weak transcription	Brain Hippocampus Middle	brain
6	chr10:93844000-93860800	Weak transcription	Psoas Muscle	Psoas
7	chr10:93845800-93856400	Weak transcription	Left Ventricle	heart
8	chr10:93847800-93861000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:93848000-93849400	Weak transcription	Fetal Kidney	kidney
10	chr10:93848000-93851000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:93848000-93851000	Weak transcription	Brain Anterior Caudate	brain
12	chr10:93848000-93851200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr10:93848000-93851400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:93848000-93851800	Weak transcription	Fetal Intestine Small	intestine
15	chr10:93848200-93851000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr10:93848200-93851200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr10:93848200-93851200	Weak transcription	GM12878-XiMat	blood
18	chr10:93848200-93860800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:93848800-93856200	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links