Variant report

Variant	rs6922822
Chromosome Location	chr6:13794044-13794045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13782601..13784296-chr6:13792088..13794112,2	MCF-7	breast:
2	chr6:13709823..13712902-chr6:13793463..13795920,4	MCF-7	breast:
3	chr6:13711644..13714237-chr6:13792795..13794426,2	K562	blood:
4	chr6:13793263..13796743-chr6:13799155..13802204,3	K562	blood:

Variant related genes	Relation type
ENSG00000050393	Chromatin interaction
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1062066	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs3734668	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66520959	0.93[ASN][1000 genomes]
rs6926691	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9396153	0.81[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6922822	CCDC90A	cis	cerebellum	SCAN
rs6922822	CCDC90A	cis	parietal	SCAN

Chromatin state (count:119 , 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	chr6:13780800-13797800	Weak transcription	Thymus	Thymus
3	chr6:13781000-13801200	Weak transcription	Psoas Muscle	Psoas
4	chr6:13781000-13802000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:13784600-13794600	Weak transcription	A549	lung
6	chr6:13785000-13800800	Weak transcription	Brain Angular Gyrus	brain
7	chr6:13785200-13801600	Weak transcription	Gastric	stomach
8	chr6:13785400-13800600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:13786000-13801200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:13786400-13794800	Weak transcription	NHLF	lung
11	chr6:13787000-13794400	Weak transcription	HMEC	breast
12	chr6:13787400-13794400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:13787400-13794400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:13787400-13794600	Strong transcription	Fetal Intestine Large	intestine
15	chr6:13787400-13794600	Strong transcription	Dnd41	blood
16	chr6:13787600-13799400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:13787800-13800600	Weak transcription	Brain Anterior Caudate	brain
18	chr6:13787800-13801200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:13788000-13794200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:13788000-13794200	Weak transcription	Osteobl	bone
21	chr6:13788000-13795600	Weak transcription	Fetal Brain Female	brain
22	chr6:13788000-13795800	Weak transcription	Fetal Brain Male	brain
23	chr6:13788000-13799000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:13788000-13799000	Weak transcription	Right Ventricle	heart
25	chr6:13788000-13799200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:13788000-13799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:13788000-13799200	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:13788000-13801200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:13788000-13802600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:13788000-13810600	Weak transcription	Fetal Heart	heart
31	chr6:13788000-13810800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:13788000-13812200	Weak transcription	Aorta	Aorta
33	chr6:13788000-13813200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:13788000-13813400	Weak transcription	Brain Germinal Matrix	brain
35	chr6:13788200-13795800	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:13788200-13807600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:13788400-13794600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:13788400-13794600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:13788400-13800800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:13788400-13801200	Weak transcription	Esophagus	oesophagus
41	chr6:13788400-13810600	Weak transcription	Colonic Mucosa	Colon
42	chr6:13788600-13794400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr6:13788600-13794800	Strong transcription	Placenta	Placenta
44	chr6:13788600-13797400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:13788600-13810800	Weak transcription	Stomach Mucosa	stomach
46	chr6:13788800-13795200	Strong transcription	Fetal Thymus	thymus
47	chr6:13788800-13810600	Weak transcription	Small Intestine	intestine
48	chr6:13788800-13812200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:13788800-13813600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:13789000-13799000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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