Variant report

Variant	rs2400731
Chromosome Location	chr3:135784871-135784872
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1278495	0.90[CEU][hapmap]
rs561307	1.00[ASW][hapmap]
rs6775793	1.00[ASW][hapmap];0.90[CEU][hapmap]
rs7630276	1.00[AFR][1000 genomes]
rs977562	1.00[AFR][1000 genomes]
rs9882561	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv4023	chr3:135772198-135816635	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2400731	PCCB	cis	cerebellum	SCAN
rs2400731	PCCB	cis	parietal	SCAN
rs2400731	TRIM42	cis	parietal	SCAN
rs2400731	PPP2R3A	cis	cerebellum	SCAN
rs2400731	LOC93432	trans	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:135761000-135802400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:135763000-135785600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:135764400-135790400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:135764800-135790400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:135765000-135786000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:135765000-135801800	Weak transcription	Esophagus	oesophagus
9	chr3:135765600-135785400	Weak transcription	Pancreas	Pancrea
10	chr3:135768800-135800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:135769800-135789400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:135769800-135789800	Weak transcription	Psoas Muscle	Psoas
13	chr3:135769800-135790000	Weak transcription	Aorta	Aorta
14	chr3:135769800-135790400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:135770000-135787200	Weak transcription	Osteobl	bone
16	chr3:135770000-135789800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:135770000-135800800	Weak transcription	Fetal Intestine Large	intestine
18	chr3:135770400-135789800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:135771200-135802000	Weak transcription	Brain Germinal Matrix	brain
20	chr3:135771200-135809600	Weak transcription	Gastric	stomach
21	chr3:135771400-135789000	Weak transcription	HSMMtube	muscle
22	chr3:135772600-135789600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:135772600-135789800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:135772600-135789800	Weak transcription	Ovary	ovary
25	chr3:135773000-135787400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:135774400-135802000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:135774600-135788800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:135774800-135789000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:135774800-135789800	Weak transcription	Left Ventricle	heart
30	chr3:135775000-135785000	Weak transcription	HSMM	muscle
31	chr3:135775000-135785200	Weak transcription	NHDF-Ad	bronchial
32	chr3:135775000-135785400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:135775000-135787600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:135775000-135788800	Weak transcription	NHEK	skin
35	chr3:135775000-135789200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:135775000-135789200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:135775000-135789400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:135775000-135789800	Weak transcription	Adipose Nuclei	Adipose
39	chr3:135775000-135809600	Weak transcription	Fetal Brain Male	brain
40	chr3:135775000-135809600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:135775200-135785200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:135775200-135788800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:135775600-135787400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:135775600-135788800	Weak transcription	Fetal Heart	heart
45	chr3:135778800-135785200	Weak transcription	Fetal Lung	lung
46	chr3:135779400-135785200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:135780600-135789800	Weak transcription	Fetal Stomach	stomach
48	chr3:135781400-135785400	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:135781400-135786400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:135781400-135786600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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