Variant report

Variant	rs7709090
Chromosome Location	chr5:68487865-68487866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68486834..68488364-chr5:68655357..68658239,2	K562	blood:
2	chr5:68487593..68492001-chr5:68493438..68496143,4	K562	blood:
3	chr5:68455037..68457035-chr5:68486114..68489088,2	K562	blood:
4	chr5:68485848..68487969-chr5:68530692..68532397,2	K562	blood:
5	chr5:68483023..68488056-chr5:68511952..68517380,10	K562	blood:

Variant related genes	Relation type
ENSG00000134056	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000265968	Chromatin interaction
ENSG00000220986	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10454825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10940208	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1128761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188874	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189395	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16875380	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271735	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17331590	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2069432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28616082	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3966728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41392244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56072942	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101109	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667192	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57047253	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176819	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58725071	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59497209	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61626775	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61699334	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61743885	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66525615	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66595384	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67275234	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67548500	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67693452	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67821207	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67980996	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890817	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767813	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767816	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767820	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767822	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767833	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72767837	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767849	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767855	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767860	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767861	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767863	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767864	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767865	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7714908	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7709090	CCDC125	cis	lung	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68485800-68493800	Weak transcription	Lung	lung
2	chr5:68486000-68489800	Weak transcription	HSMMtube	muscle
3	chr5:68486000-68498200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:68486000-68498600	Weak transcription	Left Ventricle	heart
5	chr5:68486000-68505800	Weak transcription	Ovary	ovary
6	chr5:68486000-68513600	Weak transcription	Gastric	stomach
7	chr5:68486200-68488000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:68486200-68488600	Weak transcription	Fetal Stomach	stomach
9	chr5:68486200-68489200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:68486200-68489200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:68486200-68489200	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:68486200-68490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:68486200-68490000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:68486200-68490000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:68486200-68490200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:68486200-68490200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr5:68486200-68490200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:68486200-68491200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:68486200-68492000	Weak transcription	Fetal Brain Female	brain
20	chr5:68486200-68492200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:68486200-68494200	Weak transcription	Fetal Lung	lung
22	chr5:68486200-68494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:68486200-68494600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr5:68486200-68494800	Weak transcription	Brain Substantia Nigra	brain
25	chr5:68486200-68496200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr5:68486200-68496200	Weak transcription	Brain Hippocampus Middle	brain
27	chr5:68486200-68497000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:68486200-68497600	Weak transcription	Fetal Heart	heart
29	chr5:68486200-68497600	Weak transcription	Pancreas	Pancrea
30	chr5:68486200-68498200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:68486200-68498400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:68486200-68499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:68486200-68499400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:68486200-68500200	Weak transcription	Thymus	Thymus
35	chr5:68486200-68502000	Weak transcription	Placenta	Placenta
36	chr5:68486200-68502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
38	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:68486200-68509400	Weak transcription	HSMM	muscle
42	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:68486400-68488000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:68486400-68488000	Weak transcription	Primary T cells from cord blood	blood
45	chr5:68486400-68488000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:68486400-68488000	Weak transcription	A549	lung
47	chr5:68486400-68489200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:68486400-68489200	Weak transcription	Fetal Intestine Small	intestine
49	chr5:68486400-68489400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:68486400-68490000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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