Variant report

Variant	rs1509456
Chromosome Location	chr5:42429637-42429638
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42423987..42426156-chr5:42428281..42430817,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112964	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10061299	1.00[CEU][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs10064323	0.91[ASN][1000 genomes]
rs10755268	0.99[EUR][1000 genomes]
rs10941576	0.91[ASN][1000 genomes]
rs1117110	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738365	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741390	0.82[CHD][hapmap]
rs11742495	0.92[EUR][1000 genomes]
rs11747975	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11748366	0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs11957616	0.87[EUR][1000 genomes]
rs12513643	0.89[ASN][1000 genomes]
rs12514403	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12515480	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12517368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12517931	0.89[ASN][1000 genomes]
rs12518010	0.98[ASN][1000 genomes]
rs12518274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12520318	0.89[ASN][1000 genomes]
rs12522222	0.98[ASN][1000 genomes]
rs12522421	0.98[ASN][1000 genomes]
rs12523537	0.91[ASN][1000 genomes]
rs12654242	0.87[ASN][1000 genomes]
rs13162973	0.99[EUR][1000 genomes]
rs13166255	0.81[ASN][1000 genomes]
rs13185872	0.91[ASN][1000 genomes]
rs1396768	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396773	0.99[EUR][1000 genomes]
rs1396775	0.91[ASN][1000 genomes]
rs1467049	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs1472947	0.91[ASN][1000 genomes]
rs1509452	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs1509455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509460	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1509462	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1509463	0.82[CHB][hapmap]
rs1567374	0.99[EUR][1000 genomes]
rs1605848	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1605851	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16872537	0.93[ASN][1000 genomes]
rs16872543	0.93[ASN][1000 genomes]
rs16872564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1858136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858137	0.99[EUR][1000 genomes]
rs1858138	0.93[ASN][1000 genomes]
rs1858139	0.95[EUR][1000 genomes]
rs1876788	0.99[EUR][1000 genomes]
rs1876790	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1912107	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1960498	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2036745	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2175126	0.96[EUR][1000 genomes]
rs2202883	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2221712	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395970	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498583	0.98[ASN][1000 genomes]
rs28943877	0.93[ASN][1000 genomes]
rs28943879	0.86[ASN][1000 genomes]
rs2940912	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2940914	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940916	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2940917	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940918	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2940919	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940920	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2940922	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2940923	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2940926	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2940927	0.80[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2940928	0.81[EUR][1000 genomes]
rs2940929	0.98[EUR][1000 genomes]
rs2940931	0.93[EUR][1000 genomes]
rs2940934	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940935	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs2940939	0.95[EUR][1000 genomes]
rs2940940	0.93[ASN][1000 genomes]
rs2940942	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs2940943	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs2940945	0.93[ASN][1000 genomes]
rs2972394	0.91[ASN][1000 genomes]
rs2972395	0.99[EUR][1000 genomes]
rs2972400	1.00[CEU][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs2972404	0.93[EUR][1000 genomes]
rs2972406	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972407	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972408	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2972410	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972411	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972412	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972413	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972414	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972415	0.98[EUR][1000 genomes]
rs2972416	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2972417	0.85[EUR][1000 genomes]
rs2972418	0.82[CHB][hapmap]
rs2972419	0.80[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs34509769	0.93[EUR][1000 genomes]
rs3764453	0.91[ASN][1000 genomes]
rs4358532	0.86[ASN][1000 genomes]
rs4642376	1.00[CEU][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs4866781	0.98[ASN][1000 genomes]
rs4866782	0.98[ASN][1000 genomes]
rs4866788	0.95[ASN][1000 genomes]
rs4866790	0.82[CHB][hapmap]
rs4866795	0.93[ASN][1000 genomes]
rs4866890	0.99[EUR][1000 genomes]
rs4866896	0.93[ASN][1000 genomes]
rs4866901	0.93[ASN][1000 genomes]
rs4866919	0.98[ASN][1000 genomes]
rs4866935	0.82[CHB][hapmap]
rs60126365	0.87[EUR][1000 genomes]
rs61636452	0.88[EUR][1000 genomes]
rs62370646	0.85[EUR][1000 genomes]
rs62370648	0.87[EUR][1000 genomes]
rs6451614	0.99[EUR][1000 genomes]
rs6451621	0.82[ASN][1000 genomes]
rs6876736	0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs6881436	0.97[EUR][1000 genomes]
rs6884737	0.95[EUR][1000 genomes]
rs7379192	0.99[EUR][1000 genomes]
rs7704355	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7728337	0.89[CEU][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs906817	0.93[ASN][1000 genomes]
rs9686286	0.98[EUR][1000 genomes]
rs9686537	0.91[ASN][1000 genomes]
rs9687863	0.87[ASN][1000 genomes]
rs974051	0.80[CEU][hapmap];0.90[EUR][1000 genomes]
rs979233	0.91[ASN][1000 genomes]
rs991592	0.91[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
rs1509456	GHR	cis	parietal	SCAN
rs1509456	TTC33	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42425200-42430000	Weak transcription	Aorta	Aorta
2	chr5:42425600-42434200	Weak transcription	Left Ventricle	heart
3	chr5:42426000-42430000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:42426400-42430000	Weak transcription	Right Ventricle	heart
5	chr5:42426600-42430000	Weak transcription	Ovary	ovary
6	chr5:42426600-42430000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:42426600-42430200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:42426600-42430400	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:42426600-42435200	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:42426600-42436000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:42427000-42430800	Enhancers	Liver	Liver
12	chr5:42427400-42429800	Weak transcription	Fetal Lung	lung
13	chr5:42428000-42431000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr5:42428400-42430000	Weak transcription	Fetal Intestine Small	intestine
15	chr5:42428400-42430000	Weak transcription	Psoas Muscle	Psoas
16	chr5:42428600-42430000	Weak transcription	Adipose Nuclei	Adipose
17	chr5:42429200-42431600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr5:42429400-42429800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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