Variant report

Variant	rs1894255
Chromosome Location	chr13:48989812-48989813
allele	A/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	FOSL2	chr13:48989608-48990025	A549	lung:	n/a	n/a

Variant related genes	Relation type
LPAR6	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12100135	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs12430215	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs12583516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12875750	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1573601	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs1951775	0.81[CEU][hapmap]
rs198561	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198563	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs198570	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs198584	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs198590	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs198604	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198607	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198612	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198634	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2854345	0.81[ASN][1000 genomes]
rs3020645	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs375105	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803188	0.80[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs3809328	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs3818455	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs399413	0.85[CEU][hapmap]
rs4151520	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs431406	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs471911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942765	0.81[EUR][1000 genomes]
rs520342	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7139578	0.81[CEU][hapmap]
rs9316367	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap]
rs9316369	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs9316381	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs9316388	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs9316393	1.00[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap]
rs9316395	0.81[CEU][hapmap]
rs9316399	0.81[CEU][hapmap]
rs9331991	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap]
rs943278	0.81[CEU][hapmap]
rs9526475	0.85[CEU][hapmap]
rs9534998	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs9535006	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs9535009	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs9535032	0.81[CEU][hapmap]
rs9562819	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9568032	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568033	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568034	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568035	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs990814	0.81[CEU][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	nsv1053432	chr13:48971510-48992810	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1043486	chr13:48971510-48996995	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1894255	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs1894255	ATAD2	trans	parietal	SCAN
rs1894255	ITM2B	cis	lymphoblastoid	seeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48976000-49005800	Weak transcription	Hela-S3	cervix
2	chr13:48978800-48990400	Weak transcription	Spleen	Spleen
3	chr13:48986600-48990200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:48986600-48990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:48986600-48990400	Weak transcription	Brain Germinal Matrix	brain
6	chr13:48986600-48990400	Weak transcription	Gastric	stomach
7	chr13:48986600-48990400	Weak transcription	Pancreas	Pancrea
8	chr13:48986800-48990200	Weak transcription	Lung	lung
9	chr13:48987000-48990400	Weak transcription	Fetal Brain Female	brain
10	chr13:48987000-48992800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr13:48987200-48990000	Weak transcription	Placenta	Placenta
12	chr13:48987200-48990200	Weak transcription	Small Intestine	intestine
13	chr13:48987200-48990400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:48987200-48993200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:48987400-48990200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr13:48987400-48990200	Weak transcription	Fetal Stomach	stomach
17	chr13:48987400-48990200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr13:48987400-48990400	Weak transcription	Left Ventricle	heart
19	chr13:48987400-48990600	Weak transcription	Right Ventricle	heart
20	chr13:48987400-48991200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:48987400-48991200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:48987600-48990000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr13:48987600-48990200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr13:48987600-48990200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr13:48987600-48990200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr13:48987600-48990200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:48987600-48990200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:48987600-48990200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:48987600-48990200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr13:48987600-48990200	Weak transcription	Esophagus	oesophagus
31	chr13:48987600-48990200	Weak transcription	Fetal Thymus	thymus
32	chr13:48987600-48990200	Weak transcription	Thymus	Thymus
33	chr13:48987600-48990400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr13:48987600-48990400	Weak transcription	Liver	Liver
35	chr13:48987600-48990400	Weak transcription	Ovary	ovary
36	chr13:48987600-48990600	Weak transcription	NHLF	lung
37	chr13:48987600-48991000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr13:48987600-48991200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr13:48987600-48991200	Weak transcription	HSMMtube	muscle
40	chr13:48987600-48991400	Weak transcription	Fetal Muscle Leg	muscle
41	chr13:48987600-48992800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr13:48987600-48993400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr13:48987600-48994800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr13:48987600-48995200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr13:48987600-49001800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr13:48987600-49005600	Weak transcription	Brain Hippocampus Middle	brain
47	chr13:48987600-49005800	Weak transcription	Aorta	Aorta
48	chr13:48987600-49005800	Weak transcription	HSMM	muscle
49	chr13:48987600-49010400	Weak transcription	Psoas Muscle	Psoas
50	chr13:48987800-48990000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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