Variant report

Variant	rs9366580
Chromosome Location	chr6:24711019-24711020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24710064..24711659-chr6:24781117..24783754,2	K562	blood:
2	chr6:24701416..24703004-chr6:24710087..24712359,2	MCF-7	breast:
3	chr6:24709253..24711356-chr6:24713475..24715005,2	MCF-7	breast:
4	chr6:24703121..24705782-chr6:24707406..24711144,3	MCF-7	breast:
5	chr6:24697429..24699456-chr6:24708438..24711427,3	K562	blood:
6	chr6:24707645..24711659-chr6:24779375..24784848,6	K562	blood:

Variant related genes	Relation type
ENSG00000272345	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11753290	0.87[EUR][1000 genomes]
rs17249505	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3181228	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4544900	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56344861	0.90[EUR][1000 genomes]
rs6909099	0.90[EUR][1000 genomes]
rs6917209	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6927947	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928668	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6931809	0.89[EUR][1000 genomes]
rs6937327	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6937533	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7757919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765904	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356943	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9358791	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9358793	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379685	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9366580	C6orf62	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24697800-24715800	Strong transcription	Fetal Thymus	thymus
2	chr6:24698000-24711600	Strong transcription	Primary T cells from cord blood	blood
3	chr6:24698200-24716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:24698200-24716200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:24698200-24716400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:24698400-24717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:24698600-24715200	Weak transcription	Fetal Heart	heart
9	chr6:24698600-24716200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:24698600-24716200	Weak transcription	Right Atrium	heart
11	chr6:24699000-24716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:24699000-24717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:24699600-24712800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:24699800-24712400	Strong transcription	Dnd41	blood
15	chr6:24700000-24716800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:24700200-24713200	Weak transcription	Stomach Mucosa	stomach
17	chr6:24700600-24712400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:24701000-24711400	Strong transcription	Brain Hippocampus Middle	brain
19	chr6:24701200-24711400	Strong transcription	Liver	Liver
20	chr6:24701200-24712200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:24701200-24713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:24701200-24714200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:24701400-24711400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:24701400-24712200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr6:24701400-24713000	Strong transcription	Primary B cells from cord blood	blood
26	chr6:24701400-24713000	Strong transcription	Primary hematopoietic stem cells	blood
27	chr6:24701400-24713200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:24701400-24713200	Strong transcription	Fetal Intestine Large	intestine
29	chr6:24701400-24715400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr6:24701400-24716800	Strong transcription	Placenta	Placenta
31	chr6:24701600-24712000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:24701600-24712400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:24701600-24714800	Strong transcription	HUVEC	blood vessel
34	chr6:24701600-24716200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:24701600-24716200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:24701600-24716200	Strong transcription	HMEC	breast
37	chr6:24701600-24716600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr6:24701600-24716600	Strong transcription	Fetal Muscle Leg	muscle
39	chr6:24701800-24715400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:24701800-24715600	Strong transcription	Osteobl	bone
41	chr6:24701800-24716200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:24701800-24716800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:24702000-24712000	Strong transcription	NHEK	skin
44	chr6:24702200-24711200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:24702200-24711400	Strong transcription	Brain Germinal Matrix	brain
46	chr6:24702200-24714800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:24702200-24715000	Strong transcription	NHLF	lung
48	chr6:24702200-24716400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:24702200-24716600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:24702400-24711600	Strong transcription	Adipose Nuclei	Adipose

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