Variant report

Variant	rs9830388
Chromosome Location	chr3:23559547-23559548
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	chr3:23557942..23560310-chr3:23562476..23565287,2	K562	blood:

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs11129119	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs11708160	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711072	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11715841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11718082	0.90[ASN][1000 genomes]
rs11916411	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11918529	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12386394	0.84[EUR][1000 genomes]
rs12715048	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs13064035	0.99[ASN][1000 genomes]
rs13074192	0.82[JPT][hapmap]
rs13087861	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13326048	0.86[JPT][hapmap]
rs1353322	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1498809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1498811	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1692612	0.87[ASN][1000 genomes]
rs1692620	0.86[ASN][1000 genomes]
rs1692650	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs1695200	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs17194786	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2036226	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2055310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2173460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359759	0.85[JPT][hapmap]
rs3104244	0.83[ASN][1000 genomes]
rs3111311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34080387	0.88[ASN][1000 genomes]
rs3817002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4383458	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4456808	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4484143	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4513393	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4635650	0.88[ASN][1000 genomes]
rs4858069	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4858074	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4858500	0.86[JPT][hapmap]
rs4858502	0.85[JPT][hapmap]
rs4858505	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4858506	0.86[JPT][hapmap]
rs4858509	0.90[EUR][1000 genomes]
rs55797660	0.84[EUR][1000 genomes]
rs57137870	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58748418	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60430884	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60632986	0.84[EUR][1000 genomes]
rs62256993	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62256994	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6550755	0.81[CEU][hapmap]
rs6550767	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6763329	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6763535	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6767599	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs6770079	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6770091	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs6775232	0.99[ASN][1000 genomes]
rs6776424	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6780723	0.94[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs6780787	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs6784195	0.86[JPT][hapmap]
rs6795470	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795968	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs6797907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798328	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805889	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6808513	0.94[CHB][hapmap]
rs6810100	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs704533	0.94[CHB][hapmap]
rs716456	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs73043614	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7612666	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7613091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614146	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7631334	0.85[JPT][hapmap]
rs7634117	0.92[ASN][1000 genomes]
rs7636826	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7640308	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7644666	0.90[ASN][1000 genomes]
rs7645209	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs7648443	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651893	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs778468	0.86[JPT][hapmap]
rs778475	0.87[ASN][1000 genomes]
rs778476	0.94[CHB][hapmap]
rs778477	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs778480	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs778482	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778494	0.86[JPT][hapmap]
rs778496	0.86[ASN][1000 genomes]
rs778499	0.88[CHB][hapmap]
rs778500	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs778501	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs778503	0.85[ASN][1000 genomes]
rs778510	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs778514	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs778521	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs778523	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs778526	0.87[ASN][1000 genomes]
rs952134	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs9815921	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820922	0.81[EUR][1000 genomes]
rs9821419	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9824359	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9825778	0.85[JPT][hapmap]
rs9830392	0.88[EUR][1000 genomes]
rs9830742	0.89[ASN][1000 genomes]
rs9836574	0.81[CEU][hapmap]
rs9839738	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs9847958	0.81[JPT][hapmap]
rs9856169	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9859651	0.85[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	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23540400-23560200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:23543200-23561200	Weak transcription	Psoas Muscle	Psoas
3	chr3:23550600-23560400	Weak transcription	GM12878-XiMat	blood
4	chr3:23550800-23572000	Weak transcription	Primary B cells from cord blood	blood
5	chr3:23550800-23598600	Weak transcription	HSMMtube	muscle
6	chr3:23553000-23589600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:23554400-23560000	Weak transcription	Pancreas	Pancrea
8	chr3:23558200-23560400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:23558400-23560400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:23558400-23560400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:23558400-23560400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:23558400-23560600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:23558600-23559800	Enhancers	A549	lung
14	chr3:23558600-23560200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:23558800-23560200	Enhancers	HUVEC	blood vessel
16	chr3:23558800-23560400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:23559000-23560000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:23559000-23560200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr3:23559200-23559600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:23559200-23560400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:23559200-23560600	Enhancers	Brain Substantia Nigra	brain
22	chr3:23559400-23559600	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:23559400-23560200	Enhancers	Fetal Heart	heart
24	chr3:23559400-23560400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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