Variant report

Variant	rs1874326
Chromosome Location	chr7:138157390-138157391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10155993	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10215281	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10227693	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10232771	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10247380	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10248731	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs10258706	0.91[ASN][1000 genomes]
rs1030961	0.94[CEU][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1077772	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11976614	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12112459	0.86[ASN][1000 genomes]
rs1363053	0.89[CEU][hapmap];0.84[JPT][hapmap]
rs1421604	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1544733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs1673203	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1673204	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs1673205	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1673206	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs17364560	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17461551	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1813003	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2353351	0.81[CHB][hapmap]
rs2353354	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs3757381	0.94[CEU][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778705	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs3807155	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3807156	0.88[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807157	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs55723768	0.88[ASN][1000 genomes]
rs56092804	0.88[ASN][1000 genomes]
rs57407834	0.87[ASN][1000 genomes]
rs58562866	0.86[ASN][1000 genomes]
rs62487613	0.84[ASN][1000 genomes]
rs62487615	0.91[ASN][1000 genomes]
rs62487616	0.90[ASN][1000 genomes]
rs62487619	0.88[ASN][1000 genomes]
rs6467775	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6467776	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6467778	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6467780	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6467782	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6467783	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6948094	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs6954285	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6959574	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6963539	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs6970175	0.89[ASN][1000 genomes]
rs6974877	0.89[ASN][1000 genomes]
rs728092	0.80[ASN][1000 genomes]
rs749546	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7795981	0.88[ASN][1000 genomes]
rs7808392	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs888609	0.93[ASN][1000 genomes]
rs9791462	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9791634	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs985299	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[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	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	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

Variant related diseases (count:1)

Disease	PMID	Source
Quantitative traits	19197348	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1874326	CHRM2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138146800-138163200	Weak transcription	Aorta	Aorta
2	chr7:138147000-138160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:138147000-138161400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:138147000-138162200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:138147000-138162400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:138147000-138165000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:138147200-138163200	Weak transcription	Fetal Thymus	thymus
8	chr7:138147200-138168400	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:138147200-138183800	Weak transcription	Primary B cells from cord blood	blood
10	chr7:138147200-138189000	Weak transcription	Thymus	Thymus
11	chr7:138147400-138160000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:138147600-138157400	Weak transcription	Right Atrium	heart
13	chr7:138148200-138160200	Weak transcription	Lung	lung
14	chr7:138148200-138163000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr7:138148200-138164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:138148400-138159400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:138148400-138160200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:138149800-138188600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:138150000-138159400	Weak transcription	Dnd41	blood
20	chr7:138152400-138160200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:138153400-138157400	Genic enhancers	HepG2	liver
22	chr7:138153600-138161400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr7:138153800-138157400	Weak transcription	Spleen	Spleen
24	chr7:138153800-138158600	Weak transcription	Right Ventricle	heart
25	chr7:138153800-138159400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:138153800-138159400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr7:138153800-138160600	Weak transcription	Brain Germinal Matrix	brain
28	chr7:138153800-138161800	Weak transcription	Small Intestine	intestine
29	chr7:138153800-138163200	Weak transcription	Left Ventricle	heart
30	chr7:138153800-138166200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:138153800-138184200	Weak transcription	Fetal Stomach	stomach
32	chr7:138154000-138159400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr7:138154000-138159400	Weak transcription	Brain Substantia Nigra	brain
34	chr7:138154000-138161800	Weak transcription	Brain Angular Gyrus	brain
35	chr7:138154200-138157600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr7:138154200-138161200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:138154400-138159400	Weak transcription	Brain Hippocampus Middle	brain
38	chr7:138154800-138159000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:138154800-138163800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:138154800-138167200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:138155200-138159400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:138155200-138160200	Weak transcription	Psoas Muscle	Psoas
43	chr7:138155200-138184200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr7:138155600-138159400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr7:138155600-138159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr7:138155600-138159800	Weak transcription	Stomach Mucosa	stomach
47	chr7:138155600-138160200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr7:138155800-138161400	Weak transcription	Fetal Intestine Large	intestine
49	chr7:138155800-138162000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr7:138156000-138159200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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