Variant report

Variant	rs9601240
Chromosome Location	chr13:80132373-80132374
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1208049	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1212082	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335368	0.91[ASN][1000 genomes]
rs1335370	0.89[ASN][1000 genomes]
rs1408049	0.94[ASN][1000 genomes]
rs1414155	0.96[ASN][1000 genomes]
rs1414156	0.96[ASN][1000 genomes]
rs1475797	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1577416	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1577418	0.89[ASN][1000 genomes]
rs2065743	0.94[ASN][1000 genomes]
rs2181433	0.85[ASN][1000 genomes]
rs2476172	0.86[ASN][1000 genomes]
rs2476173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484344	0.86[ASN][1000 genomes]
rs2484345	0.83[AMR][1000 genomes]
rs2760101	0.97[ASN][1000 genomes]
rs2760102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760103	0.91[ASN][1000 genomes]
rs2760105	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2760106	0.92[ASN][1000 genomes]
rs2783119	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783120	0.92[ASN][1000 genomes]
rs2783121	0.93[ASN][1000 genomes]
rs2783122	0.93[ASN][1000 genomes]
rs2783125	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2783126	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2783127	0.80[ASN][1000 genomes]
rs314688	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4145207	0.89[ASN][1000 genomes]
rs4476060	0.81[ASN][1000 genomes]
rs4885633	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4885634	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4885636	0.91[ASN][1000 genomes]
rs6563110	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6563113	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6563115	0.92[ASN][1000 genomes]
rs6563116	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs700396	0.95[ASN][1000 genomes]
rs7321953	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73235963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325095	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7338530	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7339303	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7982263	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7988601	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7990344	0.89[ASN][1000 genomes]
rs7996493	0.87[ASN][1000 genomes]
rs8002042	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9318644	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9530922	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9530925	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9545142	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9565510	0.92[ASN][1000 genomes]
rs9574429	0.81[ASN][1000 genomes]
rs9574434	0.91[ASN][1000 genomes]
rs9593399	0.81[ASN][1000 genomes]
rs9601242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987284	0.96[ASN][1000 genomes]

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	nsv916983	chr13:80065879-80249702	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1041994	chr13:80123596-80247708	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9601240	RP11-25J23.3	cis	lung	GTEx
rs9601240	RBM26	Cis_1M	lymphoblastoid	RTeQTL
rs9601240	RP11-25J23.3	cis	Thyroid	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80087400-80134000	Weak transcription	Aorta	Aorta
2	chr13:80087400-80134600	Weak transcription	Pancreas	Pancrea
3	chr13:80098600-80135000	Weak transcription	Placenta	Placenta
4	chr13:80099400-80133200	Weak transcription	Psoas Muscle	Psoas
5	chr13:80100600-80136400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:80100800-80133200	Weak transcription	Hela-S3	cervix
7	chr13:80101800-80133200	Weak transcription	Primary T cells from cord blood	blood
8	chr13:80102200-80133600	Weak transcription	Gastric	stomach
9	chr13:80104800-80133600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:80109000-80133200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr13:80109000-80133200	Weak transcription	HSMM	muscle
12	chr13:80109200-80133200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr13:80109600-80133200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr13:80110600-80133200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr13:80112600-80133200	Weak transcription	Osteobl	bone
16	chr13:80113200-80133800	Weak transcription	Left Ventricle	heart
17	chr13:80115000-80133800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:80120200-80134200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:80122000-80133200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr13:80122200-80133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:80123000-80135000	Weak transcription	Stomach Mucosa	stomach
22	chr13:80124200-80132600	Weak transcription	Fetal Kidney	kidney
23	chr13:80124200-80133000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:80124200-80133200	Weak transcription	Fetal Intestine Small	intestine
25	chr13:80124200-80133200	Weak transcription	HSMMtube	muscle
26	chr13:80124200-80133200	Weak transcription	NH-A	brain
27	chr13:80124200-80134200	Weak transcription	Fetal Intestine Large	intestine
28	chr13:80124400-80133200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:80129400-80133800	Weak transcription	Fetal Muscle Leg	muscle
30	chr13:80130000-80133000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:80130000-80134800	Strong transcription	Dnd41	blood
32	chr13:80130400-80134400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr13:80130600-80135600	ZNF genes & repeats	NHEK	skin
34	chr13:80131600-80132800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr13:80131600-80134200	Weak transcription	Fetal Thymus	thymus
36	chr13:80131600-80135200	ZNF genes & repeats	Liver	Liver
37	chr13:80131800-80132600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr13:80131800-80132600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:80131800-80132800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr13:80131800-80134200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:80131800-80135600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr13:80131800-80135600	ZNF genes & repeats	HMEC	breast
43	chr13:80132000-80134000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr13:80132000-80135800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr13:80132200-80133400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:80132200-80133600	ZNF genes & repeats	A549	lung
47	chr13:80132200-80134000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr13:80132200-80135200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr13:80132200-80136000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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