Variant report

Variant	rs812523
Chromosome Location	chr1:225743300-225743301
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10799317	0.83[ASN][1000 genomes]
rs10799318	0.85[ASN][1000 genomes]
rs10799319	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915839	0.83[ASN][1000 genomes]
rs10915847	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12028305	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2657564	0.84[ASN][1000 genomes]
rs2840958	0.84[ASN][1000 genomes]
rs3820226	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4653643	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs476540	0.87[ASN][1000 genomes]
rs487591	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498350	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs510293	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs511649	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs516249	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs551996	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554744	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554992	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs561656	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs576861	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668770	0.81[ASN][1000 genomes]
rs6751	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs712062	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524766	0.84[ASN][1000 genomes]
rs7540181	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7555139	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9804142	0.85[AMR][1000 genomes];0.81[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs812523	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
2	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
3	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225707200-225755000	Weak transcription	Gastric	stomach
5	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:225717800-225744400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:225717800-225745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
10	chr1:225717800-225758200	Weak transcription	HepG2	liver
11	chr1:225718400-225756400	Weak transcription	NHLF	lung
12	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
13	chr1:225726800-225744000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:225727400-225744400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:225727400-225747600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:225727400-225747600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:225727600-225753600	Weak transcription	NHEK	skin
18	chr1:225728000-225753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:225730000-225744400	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:225730200-225747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:225730200-225753400	Weak transcription	NHDF-Ad	bronchial
22	chr1:225730200-225753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:225730400-225744000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:225730600-225747600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
27	chr1:225732000-225744400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:225732000-225744600	Weak transcription	Fetal Intestine Large	intestine
29	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:225733000-225744400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:225733600-225744000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:225734000-225744400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:225734400-225744400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:225735200-225744400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:225735400-225746000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:225735800-225744000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:225735800-225744400	Weak transcription	A549	lung
39	chr1:225736600-225744400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:225736600-225753400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:225736600-225756200	Weak transcription	HSMMtube	muscle
42	chr1:225736800-225744200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:225737000-225744400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:225737200-225744000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:225737800-225756400	Weak transcription	Right Ventricle	heart
46	chr1:225738000-225744400	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:225738000-225747200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:225738000-225753600	Weak transcription	Aorta	Aorta
49	chr1:225738000-225753600	Weak transcription	Ovary	ovary
50	chr1:225738200-225744600	Weak transcription	Psoas Muscle	Psoas

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