Variant report

Variant	rs59697023
Chromosome Location	chr2:48542665-48542666
allele	C/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48541852..48543622-chr2:48550647..48553258,3	MCF-7	breast:
2	chr2:48010207..48012260-chr2:48541505..48544232,2	K562	blood:
3	chr2:48542620..48544627-chr2:48553697..48556453,2	K562	blood:
4	chr2:48342619..48344591-chr2:48541998..48544325,2	K562	blood:
5	chr2:48542159..48543116-chr6:26158101..26158766,2	Hela-S3	cervix:
6	chr2:48542112..48544368-chr2:48660786..48663458,2	MCF-7	breast:
7	chr2:48133540..48135075-chr2:48540885..48543276,2	K562	blood:
8	chr2:48338111..48338870-chr2:48542374..48543073,2	MCF-7	breast:
9	chr2:48540805..48543133-chr2:48691336..48694309,2	K562	blood:
10	chr2:48540677..48543829-chr2:48665802..48669252,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000116062	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10495952	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11676036	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11678403	0.83[ASN][1000 genomes]
rs11679523	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11680916	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11682633	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11684517	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11685861	0.84[ASN][1000 genomes]
rs11686007	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11687708	0.90[ASN][1000 genomes]
rs11688481	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11690690	0.84[ASN][1000 genomes]
rs11690748	0.83[ASN][1000 genomes]
rs11690845	0.84[ASN][1000 genomes]
rs12052754	0.80[ASN][1000 genomes]
rs17037289	0.81[ASN][1000 genomes]
rs17037298	0.81[EUR][1000 genomes]
rs17855177	0.84[ASN][1000 genomes]
rs4344965	0.83[ASN][1000 genomes]
rs55660911	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55761545	0.90[ASN][1000 genomes]
rs55788229	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57131168	0.99[ASN][1000 genomes]
rs57537506	0.85[ASN][1000 genomes]
rs57893565	0.82[ASN][1000 genomes]
rs58012056	0.84[ASN][1000 genomes]
rs60815228	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62137015	0.83[ASN][1000 genomes]
rs6705802	0.84[ASN][1000 genomes]
rs6718068	0.84[ASN][1000 genomes]
rs6722246	0.84[ASN][1000 genomes]
rs6743757	0.82[ASN][1000 genomes]
rs6745580	0.85[ASN][1000 genomes]
rs6756596	0.81[ASN][1000 genomes]
rs72818478	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72818488	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72818491	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72818494	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72818502	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72820403	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72820404	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72820409	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820411	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820415	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820416	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820418	0.84[ASN][1000 genomes]
rs72820420	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72820422	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820423	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72820424	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72820427	0.82[ASN][1000 genomes]
rs72820433	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72820436	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72820437	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72820439	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72820441	0.80[ASN][1000 genomes]
rs72820445	0.84[ASN][1000 genomes]
rs7562069	0.84[ASN][1000 genomes]
rs7566239	0.82[ASN][1000 genomes]
rs7573316	0.84[ASN][1000 genomes]
rs7576964	0.84[ASN][1000 genomes]
rs7577237	0.85[ASN][1000 genomes]
rs7579932	0.84[ASN][1000 genomes]
rs7600794	0.80[ASN][1000 genomes]
rs7606104	0.85[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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59697023	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48540200-48542800	Active TSS	Rectal Mucosa Donor 31	rectum
2	chr2:48540200-48543000	Active TSS	Thymus	Thymus
3	chr2:48540600-48542800	Active TSS	Rectal Smooth Muscle	rectum
4	chr2:48540600-48542800	Active TSS	Stomach Smooth Muscle	stomach
5	chr2:48540600-48542800	Active TSS	Osteobl	bone
6	chr2:48540600-48543400	Active TSS	Aorta	Aorta
7	chr2:48540600-48543400	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr2:48540600-48543400	Active TSS	Psoas Muscle	Psoas
9	chr2:48540600-48543600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:48540600-48543600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:48540600-48544000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:48540600-48544200	Active TSS	Brain Angular Gyrus	brain
13	chr2:48540600-48544600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr2:48540600-48547400	Active TSS	GM12878-XiMat	blood
15	chr2:48540800-48542800	Active TSS	Fetal Thymus	thymus
16	chr2:48540800-48543000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:48540800-48543000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr2:48540800-48543000	Active TSS	Duodenum Mucosa	Duodenum
19	chr2:48540800-48543000	Active TSS	Placenta	Placenta
20	chr2:48540800-48543200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:48540800-48543200	Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr2:48540800-48543200	Active TSS	Fetal Lung	lung
23	chr2:48540800-48543400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr2:48540800-48543600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:48540800-48543600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:48540800-48543600	Active TSS	Brain Anterior Caudate	brain
27	chr2:48540800-48543600	Active TSS	Brain Cingulate Gyrus	brain
28	chr2:48540800-48543600	Active TSS	Brain Hippocampus Middle	brain
29	chr2:48540800-48543600	Active TSS	Fetal Intestine Large	intestine
30	chr2:48540800-48543600	Active TSS	Fetal Muscle Leg	muscle
31	chr2:48540800-48543600	Active TSS	HSMMtube	muscle
32	chr2:48540800-48543600	Active TSS	NHDF-Ad	bronchial
33	chr2:48540800-48544000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:48540800-48544200	Active TSS	NHLF	lung
35	chr2:48541000-48542800	Active TSS	Fetal Stomach	stomach
36	chr2:48541000-48542800	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:48541000-48542800	Active TSS	Right Ventricle	heart
38	chr2:48541000-48542800	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr2:48541000-48543000	Active TSS	Primary monocytes fromperipheralblood	blood
40	chr2:48541000-48543000	Active TSS	Primary B cells from peripheral blood	blood
41	chr2:48541000-48543000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr2:48541000-48543000	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr2:48541000-48543200	Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr2:48541000-48543200	Active TSS	Fetal Brain Male	brain
45	chr2:48541000-48543200	Active TSS	Fetal Kidney	kidney
46	chr2:48541000-48543200	Active TSS	Placenta Amnion	Placenta Amnion
47	chr2:48541000-48543400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:48541000-48543400	Active TSS	Colon Smooth Muscle	Colon
49	chr2:48541000-48543400	Active TSS	Fetal Muscle Trunk	muscle
50	chr2:48541000-48543400	Active TSS	Ovary	ovary

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