Variant report

Variant	rs62439782
Chromosome Location	chr6:149887444-149887445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149865611..149871097-chr6:149883709..149888968,8	K562	blood:
2	chr6:149865083..149869048-chr6:149884009..149889859,10	MCF-7	breast:
3	chr6:149865819..149869096-chr6:149885709..149888757,8	MCF-7	breast:
4	chr6:149886502..149888168-chr6:150070978..150072960,2	K562	blood:
5	chr6:149863889..149870301-chr6:149880315..149888361,14	K562	blood:
6	chr6:149886717..149888905-chr6:150037583..150040474,2	MCF-7	breast:
7	chr6:149887413..149889033-chr6:149958089..149960817,2	K562	blood:
8	chr6:149884132..149889842-chr6:149966518..149971305,10	K562	blood:
9	chr6:149887426..149891060-chr6:150037726..150040656,4	K562	blood:
10	chr6:149884836..149889436-chr6:149966369..149971850,7	K562	blood:
11	chr6:149884840..149889202-chr6:150038504..150040931,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000131023	Chromatin interaction
ENSG00000186625	Chromatin interaction
ENSG00000120265	Chromatin interaction
ENSG00000131013	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1080670	0.81[AMR][1000 genomes]
rs11155671	0.81[AMR][1000 genomes]
rs2144207	0.84[ASN][1000 genomes]
rs4869923	0.85[ASN][1000 genomes]
rs4870144	0.85[AMR][1000 genomes]
rs9286597	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9322196	0.81[AMR][1000 genomes]
rs9331657	0.84[ASN][1000 genomes]
rs9377230	0.81[AMR][1000 genomes]
rs9379348	0.81[AMR][1000 genomes]
rs9399693	0.81[AMR][1000 genomes]
rs9406346	0.83[AMR][1000 genomes]
rs9485408	0.81[AMR][1000 genomes]
rs9498382	0.81[AMR][1000 genomes]
rs9689723	0.81[AMR][1000 genomes]
rs9766037	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv966665	chr6:149862756-149895103	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs62439782	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs62439782	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs62439782	RP11-350J20.5	cis	Artery Tibial	GTEx
rs62439782	GINM1	cis	lung	GTEx
rs62439782	RP11-350J20.5	cis	Thyroid	GTEx
rs62439782	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs62439782	RAET1G	cis	Thyroid	GTEx
rs62439782	GINM1	cis	Whole Blood	GTEx
rs62439782	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs62439782	RP11-350J20.5	cis	lung	GTEx
rs62439782	RP11-350J20.5	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149885800-149888400	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:149886000-149887600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:149886000-149888000	Active TSS	Stomach Smooth Muscle	stomach
4	chr6:149886000-149888200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr6:149886000-149888400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:149886000-149888600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:149886200-149887600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr6:149886200-149887600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:149886200-149887800	Active TSS	Placenta Amnion	Placenta Amnion
10	chr6:149886200-149887800	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr6:149886200-149888000	Active TSS	Primary hematopoietic stem cells	blood
12	chr6:149886200-149888000	Active TSS	Duodenum Mucosa	Duodenum
13	chr6:149886200-149888000	Active TSS	Pancreas	Pancrea
14	chr6:149886200-149888000	Active TSS	HMEC	breast
15	chr6:149886200-149888200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr6:149886200-149888200	Active TSS	Thymus	Thymus
17	chr6:149886200-149888200	Bivalent/Poised TSS	HepG2	liver
18	chr6:149886200-149888400	Active TSS	H1 Cell Line	embryonic stem cell
19	chr6:149886200-149888400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr6:149886200-149888400	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:149886200-149888400	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:149886200-149888400	Active TSS	Aorta	Aorta
23	chr6:149886200-149888400	Active TSS	Lung	lung
24	chr6:149886200-149888400	Active TSS	NHEK	skin
25	chr6:149886200-149888600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:149886200-149888600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr6:149886200-149888600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:149886200-149888600	Active TSS	Brain Anterior Caudate	brain
29	chr6:149886200-149888600	Active TSS	Colonic Mucosa	Colon
30	chr6:149886200-149888600	Active TSS	Fetal Intestine Large	intestine
31	chr6:149886200-149888800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:149886200-149888800	Active TSS	Fetal Intestine Small	intestine
33	chr6:149886200-149888800	Active TSS	Fetal Kidney	kidney
34	chr6:149886200-149888800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:149886200-149888800	Active TSS	Rectal Smooth Muscle	rectum
36	chr6:149886200-149888800	Active TSS	A549	lung
37	chr6:149886400-149887800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:149886400-149888000	Active TSS	Primary T cells fromperipheralblood	blood
39	chr6:149886400-149888000	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr6:149886400-149888000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:149886400-149888000	Active TSS	Liver	Liver
42	chr6:149886400-149888000	Active TSS	Placenta	Placenta
43	chr6:149886400-149888000	Active TSS	Fetal Thymus	thymus
44	chr6:149886400-149888200	Active TSS	Primary B cells from peripheral blood	blood
45	chr6:149886400-149888200	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr6:149886400-149888200	Active TSS	Brain Substantia Nigra	brain
47	chr6:149886400-149888200	Active TSS	Psoas Muscle	Psoas
48	chr6:149886400-149888200	Active TSS	K562	blood
49	chr6:149886400-149888400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr6:149886400-149888400	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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