Variant report

Variant	rs1544733
Chromosome Location	chr7:138230820-138230821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:138230740..138232926-chr7:138233132..138235374,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10155993	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10215281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10227693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10232771	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10247380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10248731	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10258706	0.81[ASN][1000 genomes]
rs1030961	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1077772	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs1116324	0.81[ASN][1000 genomes]
rs11976614	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12112459	0.87[ASN][1000 genomes]
rs12666310	0.91[ASN][1000 genomes]
rs1363053	0.94[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1421604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1616318	0.81[ASN][1000 genomes]
rs1659830	0.80[ASN][1000 genomes]
rs1673203	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1673204	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1673205	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1673206	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1673207	0.83[ASN][1000 genomes]
rs17364560	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs17461551	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1813003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1874326	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs2353351	0.80[CHB][hapmap]
rs2353354	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2353355	0.92[ASN][1000 genomes]
rs3757381	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778705	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs3807155	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3807156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3807157	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3816192	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55723768	0.84[ASN][1000 genomes]
rs56092804	0.84[ASN][1000 genomes]
rs57407834	0.83[ASN][1000 genomes]
rs58562866	0.87[ASN][1000 genomes]
rs62485263	0.93[ASN][1000 genomes]
rs62485264	0.91[ASN][1000 genomes]
rs62487615	0.81[ASN][1000 genomes]
rs62487616	0.82[ASN][1000 genomes]
rs62487619	0.84[ASN][1000 genomes]
rs6467776	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6467778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6467780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467782	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6467783	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6944764	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6948094	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6954285	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6959574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6963539	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6970175	0.84[ASN][1000 genomes]
rs6974877	0.84[ASN][1000 genomes]
rs728092	0.94[ASN][1000 genomes]
rs749546	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs7795981	0.84[ASN][1000 genomes]
rs7808392	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9791462	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9791634	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs985299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1544733	TRIM24	cis	parietal	SCAN
rs1544733	S100A6	trans	parietal	SCAN
rs1544733	CHRM2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138213000-138234000	Weak transcription	Brain Hippocampus Middle	brain
2	chr7:138213000-138234800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:138213000-138235200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr7:138213000-138235600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:138213000-138235800	Weak transcription	Brain Angular Gyrus	brain
6	chr7:138213000-138235800	Weak transcription	Pancreas	Pancrea
7	chr7:138213000-138235800	Weak transcription	NHDF-Ad	bronchial
8	chr7:138213000-138235800	Weak transcription	Osteobl	bone
9	chr7:138213000-138236800	Weak transcription	HSMMtube	muscle
10	chr7:138213000-138238600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:138213000-138239400	Weak transcription	Right Atrium	heart
12	chr7:138213000-138244200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:138213200-138235800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:138213200-138235800	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:138213200-138236000	Weak transcription	Right Ventricle	heart
16	chr7:138214600-138235800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:138214600-138235800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr7:138214600-138235800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:138215800-138235600	Weak transcription	Colonic Mucosa	Colon
20	chr7:138215800-138235800	Weak transcription	Spleen	Spleen
21	chr7:138216200-138235800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:138219800-138236800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:138220000-138235800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:138220200-138240400	Weak transcription	Psoas Muscle	Psoas
25	chr7:138220600-138237200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:138220800-138238400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr7:138220800-138238400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:138221000-138237000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr7:138221200-138232200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr7:138221200-138234000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:138221200-138241400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:138222000-138231000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr7:138222000-138233800	Weak transcription	Aorta	Aorta
34	chr7:138222000-138234000	Weak transcription	Lung	lung
35	chr7:138222000-138236800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr7:138222000-138238400	Weak transcription	Esophagus	oesophagus
37	chr7:138222000-138238400	Weak transcription	Gastric	stomach
38	chr7:138222200-138232400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr7:138222200-138234600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr7:138222200-138236800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:138222200-138238400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr7:138222200-138239400	Strong transcription	Fetal Thymus	thymus
43	chr7:138222400-138239400	Strong transcription	K562	blood
44	chr7:138222600-138232400	Strong transcription	HepG2	liver
45	chr7:138223600-138235800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr7:138223600-138235800	Weak transcription	Brain Substantia Nigra	brain
47	chr7:138223800-138235800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr7:138224200-138235200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:138224200-138235800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:138224200-138236800	Weak transcription	Small Intestine	intestine

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