Variant report

Variant	rs2288370
Chromosome Location	chr3:42977436-42977437
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	chr3:42976404..42980028-chr3:42981618..42984060,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYP8B1-1	chr3:42977249-42978277	ENSG00000206552

Variant related genes	Relation type
ENSG00000240747	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12494055	0.87[CHD][hapmap]
rs13078406	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13081156	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13081266	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17388512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36132109	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3732860	0.87[CHD][hapmap]
rs55946409	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6788947	0.84[CHB][hapmap]
rs9812262	0.81[JPT][hapmap]

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	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2288370	CCDC13	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42962400-42980400	Weak transcription	Placenta	Placenta
2	chr3:42975800-42977800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:42975800-42978200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:42976000-42978000	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:42976000-42978000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:42976000-42978200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr3:42976200-42977800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:42976200-42978000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:42976200-42978000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:42976400-42977800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr3:42976800-42977600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:42976800-42977800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr3:42977000-42977600	Enhancers	Gastric	stomach
14	chr3:42977000-42978600	Active TSS	Brain Anterior Caudate	brain
15	chr3:42977200-42977600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr3:42977200-42977600	Enhancers	Fetal Intestine Large	intestine
17	chr3:42977200-42978200	Enhancers	Primary T cells from cord blood	blood
18	chr3:42977200-42978200	Active TSS	Brain Angular Gyrus	brain
19	chr3:42977200-42978400	Active TSS	Brain Hippocampus Middle	brain
20	chr3:42977200-42978400	Active TSS	Stomach Smooth Muscle	stomach
21	chr3:42977400-42977600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:42977400-42977600	Active TSS	Pancreas	Pancrea
23	chr3:42977400-42977600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:42977400-42977800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:42977400-42977800	Active TSS	Fetal Brain Male	brain
26	chr3:42977400-42977800	Enhancers	Stomach Mucosa	stomach
27	chr3:42977400-42977800	Flanking Active TSS	HMEC	breast
28	chr3:42977400-42978200	Active TSS	Brain Cingulate Gyrus	brain
29	chr3:42977400-42978200	Active TSS	Fetal Lung	lung
30	chr3:42977400-42978400	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr3:42977400-42978400	Active TSS	Adipose Nuclei	Adipose
32	chr3:42977400-42978400	Active TSS	Brain Germinal Matrix	brain
33	chr3:42977400-42978400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:42977400-42978400	Active TSS	Colon Smooth Muscle	Colon
35	chr3:42977400-42978400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr3:42977400-42978400	Active TSS	Fetal Intestine Small	intestine
37	chr3:42977400-42978400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr3:42977400-42978400	Active TSS	Right Atrium	heart
39	chr3:42977400-42978400	Active TSS	NHDF-Ad	bronchial
40	chr3:42977400-42978600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:42977400-42978600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:42977400-42978600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:42977400-42978600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:42977400-42978600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:42977400-42978600	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr3:42977400-42978600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:42977400-42978600	Active TSS	Fetal Kidney	kidney
48	chr3:42977400-42978600	Active TSS	Osteobl	bone

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