Variant report

Variant	rs3859068
Chromosome Location	chr16:70408329-70408330
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70402213..70405460-chr16:70405653..70409896,4	K562	blood:
2	chr16:70380932..70385143-chr16:70404657..70409914,6	MCF-7	breast:
3	chr16:70373940..70375897-chr16:70406795..70408435,2	MCF-7	breast:
4	chr16:70406308..70408837-chr16:70511303..70514267,2	MCF-7	breast:
5	chr16:70407277..70408933-chr16:70493231..70495760,2	MCF-7	breast:
6	chr16:70406454..70409078-chr16:70491898..70493398,2	MCF-7	breast:
7	chr16:70397078..70399883-chr16:70405233..70409142,3	MCF-7	breast:
8	chr16:70402213..70407234-chr16:70407266..70410953,6	K562	blood:
9	chr16:70400513..70403701-chr16:70406827..70410088,3	MCF-7	breast:
10	chr16:70407385..70408894-chr16:70556676..70558799,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168872	Chromatin interaction
ENSG00000103051	Chromatin interaction
ENSG00000189091	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 51 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11075767	0.95[JPT][hapmap]
rs11075770	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11641683	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11645437	0.95[JPT][hapmap]
rs11645585	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11648402	1.00[JPT][hapmap]
rs11866400	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs12102803	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12446395	0.85[CEU][hapmap]
rs12447090	0.90[JPT][hapmap]
rs12597401	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12925729	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2070203	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2288491	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2303792	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2303793	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34087264	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3762171	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4284632	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4436771	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4513092	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4985407	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6499320	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7189474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7192268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7200430	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7201750	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7204583	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs722579	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs72790691	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7919	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs8049641	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs8051506	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs8052125	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8053436	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs8057610	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs8058224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8062183	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs8063690	0.99[ASN][1000 genomes]
rs8063990	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8064013	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs936994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9927553	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9936225	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9939726	0.90[EUR][1000 genomes];0.86[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	nsv482577	chr16:70329048-70516069	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv978332	chr16:70398058-70410365	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:51)

SNP	Gene	Cis/trans	Tissue	Source
rs3859068	EXOSC6	cis	normal skin	skin_eQTL
rs3859068	EXOSC6	cis	Skin Sun Exposed Lower leg	GTEx
rs3859068	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs3859068	EXOSC6	cis	lung	GTEx
rs3859068	RP11-296I10.6	cis	lung	GTEx
rs3859068	CLEC18C	cis	Whole Blood	GTEx
rs3859068	RP11-296I10.6	cis	Thyroid	GTEx
rs3859068	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs3859068	EXOSC6	cis	Esophagus Mucosa	GTEx
rs3859068	CLEC18A	cis	Artery Tibial	GTEx
rs3859068	CLEC18A	cis	lung	GTEx
rs3859068	PDXDC2P	cis	Nerve Tibial	GTEx
rs3859068	RP11-419C5.2	cis	Muscle Skeletal	GTEx
rs3859068	EXOSC6	cis	Esophagus Muscularis	GTEx
rs3859068	EXOSC6	cis	Adipose Subcutaneous	GTEx
rs3859068	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs3859068	EXOSC6	cis	Whole Blood	GTEx
rs3859068	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs3859068	EXOSC6	cis	Artery Tibial	GTEx
rs3859068	PDXDC2P	cis	Artery Aorta	GTEx
rs3859068	RP11-296I10.6	cis	Artery Tibial	GTEx
rs3859068	EXOSC6	cis	Stomach	GTEx
rs3859068	PDXDC2P	cis	Esophagus Muscularis	GTEx
rs3859068	CLEC18C	cis	Nerve Tibial	GTEx
rs3859068	RP11-296I10.6	cis	Adipose Subcutaneous	GTEx
rs3859068	RP11-296I10.6	cis	Whole Blood	GTEx
rs3859068	CLEC18C	cis	Artery Tibial	GTEx
rs3859068	CLEC18A	cis	Skin Sun Exposed Lower leg	GTEx
rs3859068	RP11-296I10.6	cis	Heart Left Ventricle	GTEx
rs3859068	PDXDC2P	cis	lung	GTEx
rs3859068	PDXDC2P	cis	Muscle Skeletal	GTEx
rs3859068	RP11-296I10.6	cis	Esophagus Muscularis	GTEx
rs3859068	PDXDC2P	cis	Artery Tibial	GTEx
rs3859068	PDXDC2P	cis	Adipose Subcutaneous	GTEx
rs3859068	CLEC18A	cis	Thyroid	GTEx
rs3859068	EXOSC6	cis	uninvolved skin	skin_eQTL
rs3859068	AARS	Cis_1M	lymphoblastoid	RTeQTL
rs3859068	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3859068	EXOSC6	cis	Thyroid	GTEx
rs3859068	EXOSC6	cis	Heart Left Ventricle	GTEx
rs3859068	RP11-419C5.2	cis	Nerve Tibial	GTEx
rs3859068	RP11-419C5.2	cis	Esophagus Muscularis	GTEx
rs3859068	EXOSC6	cis	Muscle Skeletal	GTEx
rs3859068	RP11-296I10.6	cis	Skin Sun Exposed Lower leg	GTEx
rs3859068	PDXDC2P	cis	Thyroid	GTEx
rs3859068	RP11-296I10.6	cis	Stomach	GTEx
rs3859068	CLEC18A	cis	Whole Blood	GTEx
rs3859068	EXOSC6	cis	Nerve Tibial	GTEx
rs3859068	RP11-419C5.2	cis	Adipose Subcutaneous	GTEx
rs3859068	EXOSC6	cis	Artery Aorta	GTEx
rs3859068	RP11-419C5.2	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70381600-70413200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:70381600-70414000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:70382200-70413600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:70382600-70413000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr16:70382800-70409800	Strong transcription	Fetal Muscle Leg	muscle
6	chr16:70382800-70410800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr16:70382800-70410800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr16:70383000-70410200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr16:70383000-70410600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr16:70383000-70410800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr16:70383000-70413000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr16:70383000-70413000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr16:70383000-70413000	Strong transcription	Fetal Thymus	thymus
14	chr16:70383200-70412200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr16:70383200-70413000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr16:70383200-70413400	Strong transcription	Fetal Stomach	stomach
17	chr16:70383400-70410600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:70383400-70411000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr16:70383400-70411000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr16:70383600-70412200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr16:70383600-70413200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:70383600-70413400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr16:70383600-70413600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr16:70383800-70410600	Strong transcription	Liver	Liver
25	chr16:70384400-70411000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr16:70384400-70411400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr16:70384600-70413400	Strong transcription	Fetal Intestine Small	intestine
28	chr16:70385200-70410800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr16:70385200-70410800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr16:70385400-70410200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr16:70385600-70410400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr16:70385800-70410200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr16:70386000-70413400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr16:70386200-70410400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr16:70387800-70414000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr16:70388400-70410400	Strong transcription	Left Ventricle	heart
37	chr16:70388400-70410600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:70388400-70410600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr16:70388400-70410600	Strong transcription	Fetal Intestine Large	intestine
40	chr16:70388400-70410600	Strong transcription	Placenta	Placenta
41	chr16:70388400-70410600	Strong transcription	Thymus	Thymus
42	chr16:70388400-70411000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr16:70388600-70410400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr16:70388600-70410600	Strong transcription	Lung	lung
45	chr16:70388600-70411400	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr16:70388800-70410600	Strong transcription	Spleen	Spleen
47	chr16:70389200-70410400	Strong transcription	Brain Hippocampus Middle	brain
48	chr16:70391400-70410600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr16:70393800-70413000	Weak transcription	Fetal Heart	heart
50	chr16:70394800-70408400	Strong transcription	Brain Cingulate Gyrus	brain

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