Variant report

Variant	rs1062066
Chromosome Location	chr6:13782620-13782621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13759487..13762830-chr6:13781889..13785114,3	K562	blood:
2	chr6:13708990..13711800-chr6:13781741..13784395,2	K562	blood:
3	chr6:13781829..13783763-chr6:13794136..13796516,2	K562	blood:
4	chr6:13774489..13777263-chr6:13781382..13783354,2	K562	blood:
5	chr6:13782601..13784296-chr6:13792088..13794112,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12194076	0.84[EUR][1000 genomes]
rs12209561	0.84[EUR][1000 genomes]
rs4715560	0.84[ASN][1000 genomes]
rs4715562	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4989640	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6459094	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6459095	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66520959	0.83[ASN][1000 genomes]
rs66571901	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67699103	0.84[EUR][1000 genomes]
rs6904811	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6908771	0.80[ASN][1000 genomes]
rs6922822	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs6924038	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6924799	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6926691	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs6938856	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7770141	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7772736	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9296797	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9296798	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9296799	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9367649	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382520	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9396117	0.84[ASN][1000 genomes]
rs9396153	0.90[CEU][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9464271	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9464277	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9475362	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1030774	chr6:13736025-13783733	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1062066	CCDC90A	Cis_1M	lymphoblastoid	RTeQTL
rs1062066	CCDC90A	cis	parietal	SCAN
rs1062066	ELOVL2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13766800-13802400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:13768200-13787400	Weak transcription	Fetal Lung	lung
3	chr6:13768800-13790400	Weak transcription	Lung	lung
4	chr6:13770000-13787200	Weak transcription	Fetal Stomach	stomach
5	chr6:13773200-13790200	Weak transcription	Spleen	Spleen
6	chr6:13774000-13786200	Weak transcription	Fetal Intestine Small	intestine
7	chr6:13774000-13788200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:13777200-13787200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:13777200-13787400	Weak transcription	Dnd41	blood
10	chr6:13778800-13788600	Weak transcription	Placenta	Placenta
11	chr6:13779200-13783600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:13780600-13790000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:13780600-13790000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:13780800-13789200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:13780800-13797800	Weak transcription	Thymus	Thymus
16	chr6:13781000-13801200	Weak transcription	Psoas Muscle	Psoas
17	chr6:13781000-13802000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:13781200-13790400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:13781400-13791800	Weak transcription	HSMM	muscle
20	chr6:13781600-13787600	Weak transcription	Aorta	Aorta
21	chr6:13781600-13788400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:13781600-13789200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:13782000-13787400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:13782000-13790000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:13782600-13787000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:13782600-13789800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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