Variant report

Variant	rs12098599
Chromosome Location	chr10:18965960-18965961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18940688..18942837-chr10:18963626..18966243,2	K562	blood:
2	chr10:18962456..18966517-chr10:18966877..18973376,6	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1027193	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1055116	0.84[ASN][1000 genomes]
rs10741129	0.84[ASN][1000 genomes]
rs11015435	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11540309	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11593617	0.84[AMR][1000 genomes]
rs11597737	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11812341	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11812501	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11815228	0.83[AMR][1000 genomes]
rs12762481	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12762752	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12764334	0.83[AMR][1000 genomes]
rs12764398	0.82[AMR][1000 genomes]
rs12765026	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12765238	0.83[AMR][1000 genomes]
rs12766105	0.83[AMR][1000 genomes]
rs12766314	0.83[AMR][1000 genomes]
rs12767046	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12767923	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12769425	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12770851	0.84[AMR][1000 genomes]
rs12772009	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12772522	0.85[AMR][1000 genomes]
rs12774519	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12774593	0.82[AMR][1000 genomes]
rs12775419	0.81[AMR][1000 genomes]
rs12778035	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12779018	0.90[EUR][1000 genomes]
rs12779694	0.85[AMR][1000 genomes]
rs12780652	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12781208	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12782882	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12784555	0.89[EUR][1000 genomes]
rs12784711	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12784986	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12785031	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2130531	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2171922	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2228645	0.82[AMR][1000 genomes]
rs34237250	0.95[AMR][1000 genomes]
rs34359432	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35766272	0.81[AMR][1000 genomes]
rs3740104	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4237349	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4310518	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4468242	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4573590	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4575162	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4628589	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4747355	0.81[AMR][1000 genomes]
rs4748487	0.81[AMR][1000 genomes]
rs4748490	0.82[AMR][1000 genomes]
rs4748496	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4748497	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4748498	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4748499	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55927700	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61663155	0.84[AMR][1000 genomes]
rs61842187	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6482597	0.82[ASN][1000 genomes]
rs7071300	0.84[AMR][1000 genomes]
rs7072624	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7072963	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7074644	0.84[AMR][1000 genomes]
rs7075135	0.82[AMR][1000 genomes]
rs7085318	0.84[AMR][1000 genomes]
rs7086757	0.83[AMR][1000 genomes]
rs7087030	0.80[ASN][1000 genomes]
rs7089083	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7093454	0.84[AMR][1000 genomes]
rs7096923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7099423	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7896918	0.86[ASN][1000 genomes]
rs7897159	0.95[EUR][1000 genomes]
rs7904016	0.85[AMR][1000 genomes]
rs7904949	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7905365	0.83[AMR][1000 genomes]
rs7907891	0.84[AMR][1000 genomes]
rs7909814	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7919487	0.83[AMR][1000 genomes]
rs7922005	0.89[ASN][1000 genomes]
rs7923480	0.93[AMR][1000 genomes];0.82[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
rs12098599	ARL5B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

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	chr10:18951000-18966600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:18951000-18967400	Weak transcription	Esophagus	oesophagus
5	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
6	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
8	chr10:18954000-18966600	Strong transcription	Dnd41	blood
9	chr10:18954400-18967200	Weak transcription	Gastric	stomach
10	chr10:18954400-18969200	Weak transcription	Right Ventricle	heart
11	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:18955200-18967600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:18955400-18969200	Weak transcription	Brain Angular Gyrus	brain
15	chr10:18955600-18966600	Strong transcription	Primary B cells from cord blood	blood
16	chr10:18955600-18966600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr10:18955600-18968000	Weak transcription	Brain Substantia Nigra	brain
18	chr10:18955800-18966200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr10:18955800-18966600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr10:18956000-18966200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr10:18956000-18966200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:18956000-18966600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr10:18956000-18966800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr10:18956200-18973200	Weak transcription	Small Intestine	intestine
27	chr10:18956400-18966800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr10:18956400-18967800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr10:18956800-18966600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr10:18956800-18966600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr10:18956800-18966800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:18957000-18966600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr10:18957200-18966200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr10:18957400-18968400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:18957400-18971600	Weak transcription	Fetal Heart	heart
36	chr10:18957600-18966200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:18957600-18966600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr10:18957600-18966800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr10:18957600-18966800	Strong transcription	Liver	Liver
40	chr10:18957600-18967200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr10:18957600-18969600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:18957600-18971200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:18957800-18971000	Weak transcription	Brain Anterior Caudate	brain
44	chr10:18958000-18967800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr10:18958000-18967800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr10:18958000-18968400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr10:18958200-18969800	Weak transcription	NHEK	skin
48	chr10:18958200-18970000	Weak transcription	HSMMtube	muscle
49	chr10:18958600-18966200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:18959000-18973600	Weak transcription	Left Ventricle	heart

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