Variant report

Variant	rs12762752
Chromosome Location	chr10:18950859-18950860
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr10:18950275-18951108	K562	blood:	n/a	chr10:18950399-18950408 chr10:18950981-18950994
2	POLR2A	chr10:18950575-18951332	A549	lung:	n/a	n/a
3	POLR2A	chr10:18950074-18951237	K562	blood:	n/a	n/a
4	CHD1	chr10:18946884-18951792	IMR90	lung:	n/a	chr10:18948546-18948556 chr10:18948735-18948745
5	POLR2A	chr10:18949923-18951350	HepG2	liver:	n/a	n/a
6	MAFK	chr10:18950540-18950942	HepG2	liver:	n/a	n/a
7	JUND	chr10:18950666-18951003	K562	blood:	n/a	n/a
8	POLR2A	chr10:18946803-18951639	IMR90	lung:	n/a	n/a
9	POLR2A	chr10:18950486-18951025	GM12878	blood:	n/a	n/a
10	POLR2A	chr10:18950108-18951270	GM12878	blood:	n/a	n/a
11	POLR2A	chr10:18950080-18951470	HepG2	liver:	n/a	n/a
12	POLR2A	chr10:18950705-18950913	MCF10A-Er-Src	breast:	n/a	n/a
13	WRNIP1	chr10:18950714-18951210	GM12878	blood:	n/a	n/a
14	POLR2A	chr10:18950601-18950960	K562	blood:	n/a	n/a
15	TBL1XR1	chr10:18950472-18950989	K562	blood:	n/a	n/a
16	POLR2A	chr10:18950523-18951059	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18909074..18910706-chr10:18949247..18951149,2	K562	blood:
2	chr10:18937279..18942257-chr10:18944156..18951752,16	MCF-7	breast:

Variant related genes	Relation type
ARL5B-AS1	TF binding region
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1027193	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015435	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11540309	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11593617	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11597737	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11812341	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11812501	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11815228	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12098599	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12762481	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12764334	0.84[AMR][1000 genomes]
rs12764398	0.81[AMR][1000 genomes]
rs12765026	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12765238	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12766105	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12766314	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12767046	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12767923	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12769425	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12770851	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12772009	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12772522	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12774519	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12774593	0.81[AMR][1000 genomes]
rs12778035	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12778992	0.81[AMR][1000 genomes]
rs12779018	0.85[EUR][1000 genomes]
rs12779694	0.84[AMR][1000 genomes]
rs12780652	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12781208	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12782882	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12784555	0.88[EUR][1000 genomes]
rs12784711	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12784986	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12785031	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2130531	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2171922	1.00[EUR][1000 genomes]
rs2228645	0.83[AMR][1000 genomes]
rs34237250	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34359432	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35766272	0.82[AMR][1000 genomes]
rs3740104	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4237349	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4310518	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4468242	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4573590	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4575162	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4628589	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4747355	0.84[AMR][1000 genomes]
rs4748487	0.84[AMR][1000 genomes]
rs4748490	0.85[AMR][1000 genomes]
rs4748496	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4748497	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4748498	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4748499	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55927700	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61663155	0.88[AMR][1000 genomes]
rs61842187	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7071300	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7072624	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7072963	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7074644	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7075135	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7085318	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7086757	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7089083	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7093454	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7096923	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7099423	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7896918	0.83[ASN][1000 genomes]
rs7897159	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7904016	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7904949	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7905365	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7907891	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7909814	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7919487	0.82[AMR][1000 genomes]
rs7922005	0.84[ASN][1000 genomes]
rs7923480	0.91[AMR][1000 genomes];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
rs12762752	ARL5B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18947000-18951200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr10:18947400-18951600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:18948800-18951200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:18949000-18954000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:18949400-18951000	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:18949400-18951200	Enhancers	Brain Substantia Nigra	brain
7	chr10:18949400-18951400	Flanking Active TSS	Dnd41	blood
8	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr10:18949600-18951000	Enhancers	Primary B cells from cord blood	blood
10	chr10:18949600-18951000	Enhancers	Aorta	Aorta
11	chr10:18949600-18951000	Enhancers	Brain Anterior Caudate	brain
12	chr10:18949600-18951000	Enhancers	Esophagus	oesophagus
13	chr10:18949600-18951000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr10:18949600-18951200	Enhancers	Gastric	stomach
15	chr10:18949600-18951200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr10:18949600-18951400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr10:18949600-18951400	Enhancers	Brain Hippocampus Middle	brain
18	chr10:18949600-18951400	Enhancers	Colon Smooth Muscle	Colon
19	chr10:18949600-18951400	Enhancers	Fetal Brain Male	brain
20	chr10:18949600-18951600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr10:18949600-18951800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr10:18949600-18952400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr10:18949600-18952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:18949600-18953800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:18949600-18957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr10:18949800-18951000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr10:18949800-18951000	Flanking Active TSS	Liver	Liver
29	chr10:18949800-18951000	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr10:18949800-18951000	Enhancers	Stomach Mucosa	stomach
31	chr10:18949800-18951000	Enhancers	Spleen	Spleen
32	chr10:18949800-18951200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr10:18949800-18951400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr10:18949800-18951600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr10:18949800-18952200	Enhancers	Small Intestine	intestine
36	chr10:18949800-18956600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr10:18950000-18951000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:18950000-18951000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr10:18950000-18951000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr10:18950000-18951000	Enhancers	Thymus	Thymus
41	chr10:18950000-18951200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr10:18950000-18951200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr10:18950000-18951200	Enhancers	Fetal Thymus	thymus
44	chr10:18950000-18951200	Enhancers	Pancreas	Pancrea
45	chr10:18950000-18953800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr10:18950000-18956600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr10:18950000-18957600	Weak transcription	Fetal Stomach	stomach
48	chr10:18950200-18951000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr10:18950200-18951000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr10:18950200-18951000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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