Variant report

Variant	rs12784387
Chromosome Location	chr10:18804689-18804690
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	chr1:117411254..117412990-chr10:18803618..18806039,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10508562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10508563	0.84[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs10741091	0.82[JPT][hapmap]
rs10828851	0.85[JPT][hapmap]
rs11014981	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs11015435	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs11511084	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs11815228	0.82[CHB][hapmap]
rs12762481	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs12764398	0.93[ASN][1000 genomes]
rs12766314	0.82[CHB][hapmap];0.81[YRI][hapmap]
rs12767923	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs12769425	0.83[CHB][hapmap];0.80[JPT][hapmap];0.86[YRI][hapmap]
rs12770851	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs12772522	0.83[CHB][hapmap];0.86[YRI][hapmap]
rs12774593	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs12778035	0.83[CHB][hapmap];0.80[JPT][hapmap];0.86[YRI][hapmap]
rs12779641	0.81[YRI][hapmap]
rs12781208	0.83[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs12784986	0.82[CHB][hapmap];0.81[YRI][hapmap]
rs2130531	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs2171922	0.89[JPT][hapmap];0.86[YRI][hapmap]
rs2228645	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs3740104	0.83[CHB][hapmap]
rs4237349	0.83[CHB][hapmap]
rs4314963	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4445544	0.94[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs4468242	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs4748481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4748482	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4748496	0.83[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap]
rs4748499	0.83[CHB][hapmap];0.86[YRI][hapmap]
rs6482515	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs7072624	0.83[CHB][hapmap]
rs7072963	0.85[YRI][hapmap]
rs7088091	0.85[JPT][hapmap]
rs7096923	0.82[CHB][hapmap];0.85[YRI][hapmap]
rs7099423	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs7897159	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs7898513	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.99[EUR][1000 genomes]
rs7904016	0.90[YRI][hapmap]
rs7904949	0.82[CHB][hapmap]
rs7905365	0.83[CHB][hapmap]
rs7917584	0.81[JPT][hapmap]
rs7922550	0.86[JPT][hapmap]
rs7922829	0.80[CHB][hapmap];0.86[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12784387	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs12784387	RP11-499P20.2	cis	Thyroid	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18776200-18809400	Weak transcription	Right Ventricle	heart
2	chr10:18776200-18812200	Weak transcription	Right Atrium	heart
3	chr10:18778600-18818200	Weak transcription	Fetal Intestine Small	intestine
4	chr10:18785400-18808400	Weak transcription	Colon Smooth Muscle	Colon
5	chr10:18787400-18807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:18787400-18808200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr10:18787400-18810200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:18788200-18808400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr10:18788200-18809600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:18789800-18807800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr10:18791000-18807200	Weak transcription	Brain Anterior Caudate	brain
12	chr10:18792400-18825400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr10:18794000-18818400	Weak transcription	Fetal Brain Male	brain
14	chr10:18795000-18807200	Weak transcription	Aorta	Aorta
15	chr10:18799800-18825200	Weak transcription	Colonic Mucosa	Colon
16	chr10:18800200-18826800	Weak transcription	Brain Substantia Nigra	brain
17	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:18800800-18818800	Weak transcription	Brain Germinal Matrix	brain
19	chr10:18800800-18819400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:18801000-18818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr10:18801200-18809800	Weak transcription	Brain Angular Gyrus	brain
22	chr10:18801400-18804800	Strong transcription	Fetal Lung	lung
23	chr10:18802000-18804800	Strong transcription	Left Ventricle	heart
24	chr10:18802000-18825000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:18802200-18805400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:18802400-18808400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:18802400-18809600	Weak transcription	Liver	Liver
28	chr10:18802600-18807800	Weak transcription	Fetal Stomach	stomach
29	chr10:18802600-18809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:18802600-18828200	Weak transcription	Lung	lung
32	chr10:18802800-18809400	Weak transcription	Pancreas	Pancrea
33	chr10:18803000-18807400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:18803400-18807200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:18803600-18806800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:18803600-18807200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr10:18803600-18807200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:18803600-18808600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr10:18803600-18808800	Weak transcription	Fetal Intestine Large	intestine
40	chr10:18803600-18809600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr10:18803600-18810000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr10:18803800-18809600	Weak transcription	Fetal Heart	heart
43	chr10:18804400-18807200	Weak transcription	Ovary	ovary

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