Variant report

Variant	rs10939879
Chromosome Location	chr5:60315823-60315824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60309345..60311074-chr5:60313385..60316097,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1021005	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10805374	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939881	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739952	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11740632	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12516995	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517310	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518404	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12518792	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12652830	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12652878	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12653132	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12654306	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12655209	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12655603	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1382917	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1460961	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1471488	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1479645	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526896	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs159535	0.86[EUR][1000 genomes]
rs159536	0.85[EUR][1000 genomes]
rs159537	0.88[YRI][hapmap]
rs17332824	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17392014	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17419290	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17444495	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983484	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049579	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2120956	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2120957	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28436304	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898309	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34608	0.86[EUR][1000 genomes]
rs34609	0.87[YRI][hapmap]
rs34617	0.87[YRI][hapmap]
rs34619	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs34741733	0.86[ASN][1000 genomes]
rs3797559	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4642318	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4647052	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647132	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647137	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4647150	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700397	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4700399	0.84[ASN][1000 genomes]
rs4700402	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700404	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700407	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55738840	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55814394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025209	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56031340	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56284222	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56350217	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58078456	0.81[ASN][1000 genomes]
rs58646987	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60858663	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61017995	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61101592	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62365455	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62365458	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367862	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367872	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62367878	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62367879	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62367885	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62367903	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62372103	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62372133	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62372134	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6449512	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67490467	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67555188	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67858932	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68104763	0.89[EUR][1000 genomes]
rs6884966	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs726824	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72757187	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72759206	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72759215	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7701398	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7709522	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713481	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7714396	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7722373	0.83[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7723349	0.99[ASN][1000 genomes]
rs7723901	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734205	0.87[EUR][1000 genomes]
rs7737276	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs868791	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888799	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9687099	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs976630	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs976631	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv462199	chr5:60129361-60329624	Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv598308	chr5:60129361-60329624	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv520871	chr5:60141245-60320157	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv881721	chr5:60232646-60344399	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv518695	chr5:60266875-60329624	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10939879	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs10939879	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60266200-60317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60310400-60325400	Weak transcription	Psoas Muscle	Psoas
3	chr5:60312800-60325400	Weak transcription	Left Ventricle	heart
4	chr5:60313800-60317600	Weak transcription	HSMM	muscle
5	chr5:60314000-60317000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:60314200-60318800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:60314800-60316000	Enhancers	NHEK	skin
8	chr5:60315200-60316000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:60315200-60316000	Enhancers	HUVEC	blood vessel
10	chr5:60315200-60317000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:60315400-60316400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr5:60315400-60316400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:60315400-60316600	Enhancers	A549	lung
14	chr5:60315400-60316600	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr5:60315400-60317800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:60315400-60318000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:60315600-60320000	Enhancers	NHLF	lung

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