Variant report

Variant	rs4742685
Chromosome Location	chr9:100101935-100101936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10122063	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10125198	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1020884	0.89[EUR][1000 genomes]
rs1020885	0.89[EUR][1000 genomes]
rs1037948	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1037950	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1037951	0.88[EUR][1000 genomes]
rs10435867	0.93[ASN][1000 genomes]
rs10435868	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10448274	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759624	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10759657	0.89[EUR][1000 genomes]
rs10817487	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10981890	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981919	0.89[EUR][1000 genomes]
rs10981931	0.87[EUR][1000 genomes]
rs1542506	0.87[EUR][1000 genomes]
rs1947717	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242187	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279114	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2306097	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747489	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3747493	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3747496	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3802471	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4237189	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4313271	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4366181	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4523385	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4554595	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742689	0.89[EUR][1000 genomes]
rs4742690	0.89[EUR][1000 genomes]
rs4743076	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743077	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743084	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743088	0.89[EUR][1000 genomes]
rs6478095	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6478131	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7869536	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9696167	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762823	chr9:100083872-100105782	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4742685	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs4742685	RP11-498P14.5	cis	lung	GTEx
rs4742685	ANKRD18CP	cis	Thyroid	GTEx
rs4742685	VN1R51P	cis	Thyroid	GTEx
rs4742685	RP11-520B13.4	cis	Thyroid	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100070000-100131400	Weak transcription	Fetal Kidney	kidney
2	chr9:100077000-100106400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
4	chr9:100080400-100126400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr9:100083800-100124000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:100086400-100110400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:100086600-100121600	Weak transcription	Right Ventricle	heart
8	chr9:100086600-100132000	Weak transcription	Thymus	Thymus
9	chr9:100086800-100104000	Weak transcription	Dnd41	blood
10	chr9:100088000-100126200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr9:100088200-100127000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:100088600-100128600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:100088600-100132800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:100088800-100103800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:100088800-100121400	Weak transcription	Gastric	stomach
16	chr9:100089000-100104000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:100089000-100104000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:100089200-100102800	Weak transcription	Fetal Intestine Small	intestine
19	chr9:100089200-100128200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:100090600-100104200	Weak transcription	Liver	Liver
21	chr9:100090600-100119000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:100090600-100133800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr9:100091000-100102600	Weak transcription	Lung	lung
24	chr9:100091200-100106400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:100091600-100102800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr9:100091600-100103000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:100091600-100103800	Weak transcription	Spleen	Spleen
28	chr9:100091600-100106400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:100091600-100149200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr9:100092000-100105400	Weak transcription	Primary T cells from cord blood	blood
31	chr9:100093000-100102800	Weak transcription	Fetal Stomach	stomach
32	chr9:100093000-100104000	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:100093000-100105600	Weak transcription	Fetal Lung	lung
34	chr9:100093000-100111000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:100093000-100117000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:100093600-100102800	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:100093600-100103800	Weak transcription	Aorta	Aorta
38	chr9:100093600-100106400	Weak transcription	Left Ventricle	heart
39	chr9:100093600-100122400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr9:100093800-100104000	Weak transcription	Ovary	ovary
41	chr9:100094600-100109400	Weak transcription	Brain Angular Gyrus	brain
42	chr9:100095200-100102800	Weak transcription	Brain Germinal Matrix	brain
43	chr9:100095200-100105400	Weak transcription	Brain Anterior Caudate	brain
44	chr9:100095600-100116800	Weak transcription	Brain Hippocampus Middle	brain
45	chr9:100095800-100109200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:100096800-100109400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:100097200-100104000	Weak transcription	Adipose Nuclei	Adipose
48	chr9:100097400-100102800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:100097400-100104800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr9:100099000-100132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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