Variant report

Variant	rs11682838
Chromosome Location	chr2:48641155-48641156
allele	A/G
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: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10182093	0.87[EUR][1000 genomes]
rs10191938	0.87[EUR][1000 genomes]
rs10195717	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs10197359	0.89[EUR][1000 genomes]
rs11674217	0.82[EUR][1000 genomes]
rs11674317	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11674683	1.00[AFR][1000 genomes]
rs11675947	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11676078	0.82[EUR][1000 genomes]
rs11676925	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11677205	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11677350	1.00[AFR][1000 genomes]
rs11678825	0.83[EUR][1000 genomes]
rs11678934	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11679518	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11679685	0.90[EUR][1000 genomes]
rs11680968	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11683202	0.82[EUR][1000 genomes]
rs11687276	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11687401	1.00[AFR][1000 genomes]
rs11687461	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11687851	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11688465	1.00[AFR][1000 genomes]
rs11691302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11691407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11692537	0.82[EUR][1000 genomes]
rs11694094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11694955	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13398456	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs17325698	1.00[AFR][1000 genomes]
rs17397094	1.00[AFR][1000 genomes]
rs17397449	0.86[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17397707	1.00[AFR][1000 genomes]
rs28505584	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4364065	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs72889641	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7573281	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7584796	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs952468	0.89[CEU][hapmap];1.00[AFR][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
rs11682838	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	chr2:48639400-48641800	Enhancers	HepG2	liver
15	chr2:48639400-48642200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:48639600-48642000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:48639600-48645200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:48639600-48647400	Enhancers	Liver	Liver
19	chr2:48640000-48642200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:48640000-48642200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:48640000-48642200	Enhancers	Brain Cingulate Gyrus	brain
22	chr2:48640000-48643600	Enhancers	Fetal Intestine Large	intestine
23	chr2:48640000-48646200	Enhancers	Fetal Intestine Small	intestine
24	chr2:48640400-48642200	Enhancers	Adipose Nuclei	Adipose
25	chr2:48640400-48642200	Weak transcription	Fetal Lung	lung
26	chr2:48640400-48642200	Weak transcription	Spleen	Spleen
27	chr2:48640400-48642400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:48640400-48642800	Weak transcription	Fetal Kidney	kidney
29	chr2:48640400-48647600	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:48640400-48647600	Weak transcription	Ovary	ovary
31	chr2:48640600-48641600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:48640600-48641800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:48640600-48642000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:48640600-48642000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:48640600-48642000	Weak transcription	NHDF-Ad	bronchial
36	chr2:48640600-48642200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:48640600-48642200	Weak transcription	Right Atrium	heart
38	chr2:48640600-48647800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:48640800-48641200	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:48640800-48641800	Weak transcription	Brain Angular Gyrus	brain
41	chr2:48640800-48642000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:48640800-48642000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:48640800-48642200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:48640800-48642200	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:48640800-48643400	Weak transcription	Fetal Stomach	stomach
46	chr2:48641000-48641400	Weak transcription	Brain Substantia Nigra	brain
47	chr2:48641000-48642000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:48641000-48642200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:48641000-48642200	Weak transcription	Right Ventricle	heart
50	chr2:48641000-48647400	Weak transcription	Stomach Smooth Muscle	stomach

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