Variant report

Variant	rs6493809
Chromosome Location	chr15:56004641-56004642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56002955..56005054-chr15:56005105..56008036,2	MCF-7	breast:
2	chr15:56002613..56005532-chr15:56007469..56010222,2	K562	blood:
3	chr15:55999212..56002187-chr15:56002535..56005637,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10518817	0.81[CHB][hapmap]
rs10851589	0.81[CHB][hapmap]
rs10851591	0.93[ASN][1000 genomes]
rs11630141	0.90[ASN][1000 genomes]
rs11854213	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs12373006	0.85[CHB][hapmap]
rs12442771	0.90[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs12591246	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs16976428	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs16976472	0.81[CHB][hapmap]
rs1814329	0.91[CHB][hapmap]
rs2008336	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2118781	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs2414424	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2414426	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2414427	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2414430	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2414431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28485308	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28575567	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4377101	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774802	0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4774803	0.92[ASN][1000 genomes]
rs57782071	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59820715	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62043907	0.82[ASN][1000 genomes]
rs62043908	0.84[ASN][1000 genomes]
rs6493807	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493814	0.90[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs71110312	0.84[ASN][1000 genomes]
rs715321	0.83[ASN][1000 genomes]
rs7161967	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7162071	0.85[CEU][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs7162371	0.93[ASN][1000 genomes]
rs7163167	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs7171318	0.81[CHB][hapmap]
rs7172903	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178379	0.81[CHB][hapmap]
rs7181212	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182733	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs7359255	0.91[CHB][hapmap]
rs8023911	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8025445	0.90[CHB][hapmap]
rs8030795	0.85[ASN][1000 genomes]
rs8034414	0.90[ASN][1000 genomes]
rs8037136	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8038074	0.80[ASN][1000 genomes]
rs8042029	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 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	chr15:55996200-56015000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:55996400-56007600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:55996600-56004800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:55996600-56005400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:55999000-56005000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:55999800-56028000	Weak transcription	Fetal Kidney	kidney
7	chr15:56001000-56007600	Weak transcription	Hela-S3	cervix
8	chr15:56001200-56007600	Weak transcription	HepG2	liver
9	chr15:56002200-56007400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:56002200-56014600	Weak transcription	A549	lung
11	chr15:56003400-56011400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:56003800-56008000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:56004000-56007800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:56004000-56008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:56004000-56012800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:56004400-56011000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:56004600-56004800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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