Variant report

Variant	rs55640438
Chromosome Location	chr2:48640793-48640794
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	chr2:48633890..48635428-chr2:48640629..48643120,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10208627	0.83[ASN][1000 genomes]
rs10211336	0.92[ASN][1000 genomes]
rs10454133	0.98[ASN][1000 genomes]
rs10454134	0.98[ASN][1000 genomes]
rs11680719	0.94[ASN][1000 genomes]
rs11683639	0.94[ASN][1000 genomes]
rs11683708	0.92[ASN][1000 genomes]
rs11689622	0.92[ASN][1000 genomes]
rs12105983	0.83[ASN][1000 genomes]
rs13399936	0.95[ASN][1000 genomes]
rs13400909	0.94[ASN][1000 genomes]
rs13401749	0.94[ASN][1000 genomes]
rs13401752	0.94[ASN][1000 genomes]
rs13429377	0.83[AFR][1000 genomes]
rs4274640	0.94[ASN][1000 genomes]
rs4316980	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4438532	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4494796	0.97[ASN][1000 genomes]
rs4606978	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4638844	0.88[ASN][1000 genomes]
rs55757090	0.89[ASN][1000 genomes]
rs55971719	0.89[ASN][1000 genomes]
rs56365822	0.87[ASN][1000 genomes]
rs58020097	0.94[ASN][1000 genomes]
rs58969359	0.94[ASN][1000 genomes]
rs58978223	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59045263	0.83[ASN][1000 genomes]
rs60042255	0.87[ASN][1000 genomes]
rs60988618	0.95[ASN][1000 genomes]
rs61303367	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62137018	0.89[ASN][1000 genomes]
rs62137019	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62137021	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137041	0.97[ASN][1000 genomes]
rs66705539	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6732196	0.96[ASN][1000 genomes]
rs6735288	0.83[ASN][1000 genomes]
rs6747441	0.86[ASN][1000 genomes]
rs6749773	0.87[ASN][1000 genomes]
rs72820454	0.87[ASN][1000 genomes]
rs72820474	0.98[ASN][1000 genomes]
rs72820479	0.97[ASN][1000 genomes]
rs72820484	0.95[ASN][1000 genomes]
rs72820492	0.93[ASN][1000 genomes]
rs72820494	0.94[ASN][1000 genomes]
rs72820499	0.94[ASN][1000 genomes]
rs7565792	0.92[ASN][1000 genomes]
rs7568574	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55640438	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48634000-48641400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:48634400-48641800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:48634600-48641400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:48634600-48642200	Weak transcription	Small Intestine	intestine
5	chr2:48635600-48641400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:48637200-48642200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:48637800-48642400	Weak transcription	A549	lung
8	chr2:48638200-48642200	Weak transcription	Left Ventricle	heart
9	chr2:48638400-48641800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:48638400-48641800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:48638400-48642400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:48638400-48643400	Weak transcription	Gastric	stomach
13	chr2:48639200-48642200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:48639400-48640800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:48639400-48640800	Enhancers	Fetal Stomach	stomach
16	chr2:48639400-48641800	Enhancers	HepG2	liver
17	chr2:48639400-48642200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:48639600-48641000	Enhancers	Brain Substantia Nigra	brain
19	chr2:48639600-48642000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:48639600-48645200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr2:48639600-48647400	Enhancers	Liver	Liver
22	chr2:48639800-48640800	Enhancers	Brain Hippocampus Middle	brain
23	chr2:48640000-48640800	Enhancers	Brain Angular Gyrus	brain
24	chr2:48640000-48640800	Enhancers	Fetal Muscle Leg	muscle
25	chr2:48640000-48642200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:48640000-48642200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:48640000-48642200	Enhancers	Brain Cingulate Gyrus	brain
28	chr2:48640000-48643600	Enhancers	Fetal Intestine Large	intestine
29	chr2:48640000-48646200	Enhancers	Fetal Intestine Small	intestine
30	chr2:48640200-48640800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:48640200-48640800	Enhancers	Aorta	Aorta
32	chr2:48640200-48640800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:48640200-48640800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:48640400-48642200	Enhancers	Adipose Nuclei	Adipose
35	chr2:48640400-48642200	Weak transcription	Fetal Lung	lung
36	chr2:48640400-48642200	Weak transcription	Spleen	Spleen
37	chr2:48640400-48642400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:48640400-48642800	Weak transcription	Fetal Kidney	kidney
39	chr2:48640400-48647600	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:48640400-48647600	Weak transcription	Ovary	ovary
41	chr2:48640600-48640800	Enhancers	Right Ventricle	heart
42	chr2:48640600-48641000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:48640600-48641600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:48640600-48641800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:48640600-48642000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:48640600-48642000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:48640600-48642000	Weak transcription	NHDF-Ad	bronchial
48	chr2:48640600-48642200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:48640600-48642200	Weak transcription	Right Atrium	heart
50	chr2:48640600-48647800	Weak transcription	Rectal Smooth Muscle	rectum

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