Variant report

Variant	rs12209561
Chromosome Location	chr6:13767783-13767784
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	chr6:13710677..13712820-chr6:13763898..13768186,3	K562	blood:
2	chr6:13750883..13753815-chr6:13765180..13768175,2	K562	blood:

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1062066	0.84[EUR][1000 genomes]
rs12194076	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715562	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4989640	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6459094	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6459095	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66571901	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67699103	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904811	0.88[EUR][1000 genomes]
rs6924038	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6924799	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7770141	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7772736	0.89[EUR][1000 genomes]
rs9296797	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9296798	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296799	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9367649	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382501	0.85[ASN][1000 genomes]
rs9382520	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9396153	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9464271	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9464277	0.90[EUR][1000 genomes]
rs9475361	0.85[AMR][1000 genomes]
rs9475362	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12209561	CCDC90A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13763800-13768000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:13764400-13768200	Enhancers	Dnd41	blood
3	chr6:13764600-13767800	Weak transcription	Pancreas	Pancrea
4	chr6:13764600-13768600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:13765800-13768800	Enhancers	Fetal Thymus	thymus
6	chr6:13766000-13768200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:13766000-13768200	Enhancers	Placenta	Placenta
8	chr6:13766400-13768000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:13766400-13768200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:13766600-13767800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr6:13766600-13767800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:13766600-13768000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr6:13766600-13768400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:13766800-13768000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:13766800-13772800	Weak transcription	Spleen	Spleen
16	chr6:13766800-13802400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:13767200-13767800	Enhancers	Primary B cells from peripheral blood	blood
18	chr6:13767200-13767800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:13767200-13768000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:13767200-13768800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:13767400-13767800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:13767400-13767800	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr6:13767400-13767800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:13767400-13767800	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr6:13767400-13768000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:13767400-13768000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:13767400-13768000	Active TSS	Brain Cingulate Gyrus	brain
28	chr6:13767400-13768000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
29	chr6:13767400-13768200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr6:13767400-13768200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:13767400-13768200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:13767400-13768200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr6:13767400-13768200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:13767400-13768200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:13767400-13768200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:13767400-13768200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr6:13767400-13768200	Flanking Active TSS	Fetal Heart	heart
38	chr6:13767400-13768200	Active TSS	Ovary	ovary
39	chr6:13767400-13768200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr6:13767400-13768200	Enhancers	HMEC	breast
41	chr6:13767400-13768200	Flanking Active TSS	HSMMtube	muscle
42	chr6:13767400-13768200	Enhancers	K562	blood
43	chr6:13767400-13768200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr6:13767400-13768200	Flanking Active TSS	NHDF-Ad	bronchial
45	chr6:13767400-13768200	Flanking Active TSS	Osteobl	bone
46	chr6:13767400-13768600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:13767600-13767800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:13767600-13767800	Enhancers	Primary B cells from cord blood	blood
49	chr6:13767600-13767800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr6:13767600-13767800	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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