Variant report

Variant	rs12779018
Chromosome Location	chr10:18968668-18968669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18938885..18940645-chr10:18967631..18969812,2	K562	blood:
2	chr10:18962456..18966517-chr10:18966877..18973376,6	K562	blood:
3	chr10:18966816..18969348-chr10:18971030..18973085,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CACNB2-1	chr10:18967049-18970567	NONHSAT011652

Variant related genes	Relation type
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1027193	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11015435	0.85[EUR][1000 genomes]
rs11540309	0.90[EUR][1000 genomes]
rs11597110	0.92[AMR][1000 genomes]
rs11597737	0.85[EUR][1000 genomes]
rs11812501	0.90[EUR][1000 genomes]
rs12098599	0.90[EUR][1000 genomes]
rs12762481	0.80[EUR][1000 genomes]
rs12762752	0.85[EUR][1000 genomes]
rs12764299	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12765026	0.90[EUR][1000 genomes]
rs12767046	0.87[AFR][1000 genomes]
rs12768464	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12773254	0.88[AMR][1000 genomes]
rs12780652	0.84[EUR][1000 genomes]
rs12780826	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12782882	0.90[EUR][1000 genomes]
rs12784555	0.97[EUR][1000 genomes]
rs12784711	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1880681	0.93[AMR][1000 genomes]
rs2130531	0.85[EUR][1000 genomes]
rs2171922	0.85[EUR][1000 genomes]
rs3740104	0.83[EUR][1000 genomes]
rs4310518	0.87[EUR][1000 genomes]
rs61842187	0.85[EUR][1000 genomes]
rs7072624	0.86[EUR][1000 genomes]
rs7072963	0.85[EUR][1000 genomes]
rs7096923	0.89[EUR][1000 genomes]
rs7897159	0.85[EUR][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	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
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12779018	ARL5B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
4	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
6	chr10:18954400-18969200	Weak transcription	Right Ventricle	heart
7	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:18955400-18969200	Weak transcription	Brain Angular Gyrus	brain
10	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:18956200-18973200	Weak transcription	Small Intestine	intestine
13	chr10:18957400-18971600	Weak transcription	Fetal Heart	heart
14	chr10:18957600-18969600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:18957600-18971200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:18957800-18971000	Weak transcription	Brain Anterior Caudate	brain
17	chr10:18958200-18969800	Weak transcription	NHEK	skin
18	chr10:18958200-18970000	Weak transcription	HSMMtube	muscle
19	chr10:18959000-18973600	Weak transcription	Left Ventricle	heart
20	chr10:18960000-18972400	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:18960200-18969800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:18960400-18970200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr10:18960800-18970200	Weak transcription	NHLF	lung
24	chr10:18960800-18973400	Weak transcription	Ovary	ovary
25	chr10:18961000-18970800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:18961000-18973600	Weak transcription	Thymus	Thymus
27	chr10:18961600-18971000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr10:18961800-18970200	Weak transcription	HMEC	breast
29	chr10:18962400-18973600	Weak transcription	Fetal Intestine Small	intestine
30	chr10:18962400-18973600	Weak transcription	Fetal Stomach	stomach
31	chr10:18963200-18973400	Weak transcription	Pancreas	Pancrea
32	chr10:18963800-18970000	Weak transcription	NHDF-Ad	bronchial
33	chr10:18964000-18972200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr10:18964000-18973000	Weak transcription	Primary T cells from cord blood	blood
35	chr10:18964200-18973400	Weak transcription	Psoas Muscle	Psoas
36	chr10:18964600-18973600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr10:18964600-18973800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr10:18964800-18969800	Weak transcription	Osteobl	bone
39	chr10:18964800-18970000	Weak transcription	A549	lung
40	chr10:18964800-18970400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr10:18964800-18970800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr10:18964800-18973400	Weak transcription	Fetal Brain Female	brain
43	chr10:18964800-18973400	Weak transcription	HUVEC	blood vessel
44	chr10:18964800-18973800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr10:18965000-18972800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr10:18965000-18973400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr10:18965200-18970000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:18965200-18971600	Weak transcription	Placenta	Placenta
49	chr10:18965200-18972200	Weak transcription	Fetal Muscle Leg	muscle
50	chr10:18965200-18972400	Weak transcription	Colon Smooth Muscle	Colon

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