Variant report

Variant	rs3734668
Chromosome Location	chr6:13790393-13790394
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13615016..13616949-chr6:13788580..13791434,2	MCF-7	breast:
2	chr6:13711228..13713635-chr6:13789081..13791410,2	MCF-7	breast:
3	chr6:13710394..13713005-chr6:13788901..13792554,4	MCF-7	breast:
4	chr6:13614177..13616192-chr6:13789312..13791001,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC90A-8	chr6:13786977-13790645	NONHSAT107814

Variant related genes	Relation type
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs66520959	0.93[ASN][1000 genomes]
rs6922822	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926691	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3734668	CCDC90A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13766800-13802400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:13768800-13790400	Weak transcription	Lung	lung
3	chr6:13780800-13797800	Weak transcription	Thymus	Thymus
4	chr6:13781000-13801200	Weak transcription	Psoas Muscle	Psoas
5	chr6:13781000-13802000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:13781200-13790400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:13781400-13791800	Weak transcription	HSMM	muscle
8	chr6:13784600-13792000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:13784600-13794600	Weak transcription	A549	lung
10	chr6:13785000-13800800	Weak transcription	Brain Angular Gyrus	brain
11	chr6:13785200-13801600	Weak transcription	Gastric	stomach
12	chr6:13785400-13800600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:13786000-13801200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:13786400-13794800	Weak transcription	NHLF	lung
15	chr6:13787000-13794400	Weak transcription	HMEC	breast
16	chr6:13787200-13792400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:13787400-13790400	Weak transcription	Fetal Stomach	stomach
18	chr6:13787400-13790600	Strong transcription	Primary B cells from cord blood	blood
19	chr6:13787400-13794400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:13787400-13794400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:13787400-13794600	Strong transcription	Fetal Intestine Large	intestine
22	chr6:13787400-13794600	Strong transcription	Dnd41	blood
23	chr6:13787600-13792200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:13787600-13799400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:13787800-13800600	Weak transcription	Brain Anterior Caudate	brain
26	chr6:13787800-13801200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:13788000-13792200	Weak transcription	Brain Substantia Nigra	brain
28	chr6:13788000-13794000	Weak transcription	NH-A	brain
29	chr6:13788000-13794200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:13788000-13794200	Weak transcription	Osteobl	bone
31	chr6:13788000-13795600	Weak transcription	Fetal Brain Female	brain
32	chr6:13788000-13795800	Weak transcription	Fetal Brain Male	brain
33	chr6:13788000-13799000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:13788000-13799000	Weak transcription	Right Ventricle	heart
35	chr6:13788000-13799200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:13788000-13799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:13788000-13799200	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:13788000-13801200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr6:13788000-13802600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:13788000-13810600	Weak transcription	Fetal Heart	heart
41	chr6:13788000-13810800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:13788000-13812200	Weak transcription	Aorta	Aorta
43	chr6:13788000-13813200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:13788000-13813400	Weak transcription	Brain Germinal Matrix	brain
45	chr6:13788200-13793600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:13788200-13794000	Strong transcription	Fetal Muscle Leg	muscle
47	chr6:13788200-13795800	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:13788200-13807600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:13788400-13790400	Weak transcription	Hela-S3	cervix
50	chr6:13788400-13794600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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