Variant report

Variant	rs2972400
Chromosome Location	chr5:42425830-42425831
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42425732..42427236-chr5:42432145..42434745,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10061299	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10755268	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117110	0.92[EUR][1000 genomes]
rs11738365	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11742495	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747975	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748366	0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957616	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162973	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396768	0.95[EUR][1000 genomes]
rs1396773	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1467049	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509452	0.80[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509453	1.00[ASN][1000 genomes]
rs1509455	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1509456	1.00[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs1567374	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605848	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1605851	0.92[EUR][1000 genomes]
rs1858136	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1858137	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858139	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876788	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876790	1.00[CEU][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs1912107	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960498	0.89[CEU][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2036745	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2175126	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202883	0.91[EUR][1000 genomes]
rs2221712	0.91[EUR][1000 genomes]
rs2395970	0.92[EUR][1000 genomes]
rs2940912	0.99[EUR][1000 genomes]
rs2940914	0.92[EUR][1000 genomes]
rs2940916	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940917	0.89[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2940918	0.89[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2940919	0.89[CEU][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2940920	0.89[CEU][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940922	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2940926	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940928	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2940929	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940931	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940934	0.92[EUR][1000 genomes]
rs2940935	0.80[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940939	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2940942	0.80[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940943	0.80[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972391	1.00[ASN][1000 genomes]
rs2972395	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972404	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972406	0.89[EUR][1000 genomes]
rs2972407	0.89[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2972410	0.90[EUR][1000 genomes]
rs2972411	0.89[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2972412	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs2972413	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2972414	0.85[EUR][1000 genomes]
rs2972415	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972416	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2972417	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972419	0.87[ASW][hapmap];0.80[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34509769	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4642376	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866890	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58416991	1.00[ASN][1000 genomes]
rs58960035	1.00[ASN][1000 genomes]
rs60126365	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61636452	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370642	1.00[ASN][1000 genomes]
rs62370646	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370648	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451614	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876736	0.88[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881436	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884737	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7379192	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704355	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728337	0.89[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686286	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974051	0.80[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv881375	chr5:42254097-42442715	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2972400	GHR	cis	parietal	SCAN
rs2972400	TTC33	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42423000-42426000	Active TSS	Right Atrium	heart
2	chr5:42423400-42426400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:42424600-42426600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr5:42424800-42426200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr5:42424800-42426400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr5:42424800-42427000	Flanking Active TSS	Liver	Liver
7	chr5:42425200-42428000	Weak transcription	Gastric	stomach
8	chr5:42425200-42430000	Weak transcription	Aorta	Aorta
9	chr5:42425400-42426000	Flanking Active TSS	Colon Smooth Muscle	Colon
10	chr5:42425400-42426000	Active TSS	Fetal Intestine Small	intestine
11	chr5:42425400-42426400	Weak transcription	Placenta	Placenta
12	chr5:42425400-42426600	Enhancers	Fetal Heart	heart
13	chr5:42425400-42428200	Weak transcription	Spleen	Spleen
14	chr5:42425400-42429200	Weak transcription	Esophagus	oesophagus
15	chr5:42425600-42426000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:42425600-42426000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:42425600-42426000	Enhancers	Ovary	ovary
18	chr5:42425600-42426600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr5:42425600-42426600	Enhancers	Fetal Muscle Leg	muscle
20	chr5:42425600-42426600	Enhancers	Psoas Muscle	Psoas
21	chr5:42425600-42426600	Enhancers	Rectal Smooth Muscle	rectum
22	chr5:42425600-42434200	Weak transcription	Left Ventricle	heart
23	chr5:42425800-42426200	Flanking Active TSS	Fetal Lung	lung
24	chr5:42425800-42426200	Weak transcription	Right Ventricle	heart
25	chr5:42425800-42426600	Enhancers	Fetal Stomach	stomach
26	chr5:42425800-42426600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:42425800-42426800	Enhancers	Duodenum Smooth Muscle	Duodenum

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