Variant report

Variant	rs1876790
Chromosome Location	chr5:42422855-42422856
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	chr5:42422660..42423547-chr5:42514575..42515445,3	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10061299	1.00[CEU][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs10064323	0.96[ASN][1000 genomes]
rs10755268	0.99[EUR][1000 genomes]
rs10941576	0.96[ASN][1000 genomes]
rs1117110	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11738365	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
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	0.94[ASN][1000 genomes]
rs12514403	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12515480	0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12517368	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12517931	0.94[ASN][1000 genomes]
rs12518010	0.93[ASN][1000 genomes]
rs12518274	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12520318	0.94[ASN][1000 genomes]
rs12522222	0.93[ASN][1000 genomes]
rs12522421	0.93[ASN][1000 genomes]
rs12523537	0.96[ASN][1000 genomes]
rs12654242	0.93[ASN][1000 genomes]
rs13162973	0.99[EUR][1000 genomes]
rs13185872	0.96[ASN][1000 genomes]
rs1396768	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1396773	0.99[EUR][1000 genomes]
rs1396775	0.96[ASN][1000 genomes]
rs1467049	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs1472947	0.96[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1509456	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]
rs1509460	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1509462	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1567374	0.99[EUR][1000 genomes]
rs1605848	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1605851	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16872537	0.98[ASN][1000 genomes]
rs16872543	0.98[ASN][1000 genomes]
rs16872564	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1858136	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1858137	0.99[EUR][1000 genomes]
rs1858138	0.98[ASN][1000 genomes]
rs1858139	0.95[EUR][1000 genomes]
rs1876788	0.99[EUR][1000 genomes]
rs1912107	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1960498	0.94[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1979994	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2036745	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2175126	0.96[EUR][1000 genomes]
rs2202883	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2221712	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2395970	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28498583	0.93[ASN][1000 genomes]
rs28943877	0.98[ASN][1000 genomes]
rs28943879	0.80[ASN][1000 genomes]
rs2940912	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2940914	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2940916	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2940917	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2940918	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2940919	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2940920	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2940922	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2940923	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2940926	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2940927	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2940928	0.81[EUR][1000 genomes]
rs2940929	0.98[EUR][1000 genomes]
rs2940931	0.93[EUR][1000 genomes]
rs2940934	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2940935	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs2940939	0.95[EUR][1000 genomes]
rs2940940	0.98[ASN][1000 genomes]
rs2940942	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs2940943	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs2940945	0.98[ASN][1000 genomes]
rs2972394	0.96[ASN][1000 genomes]
rs2972395	0.99[EUR][1000 genomes]
rs2972400	1.00[CEU][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs2972404	0.93[EUR][1000 genomes]
rs2972406	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972407	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972408	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2972410	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972411	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972412	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972413	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972414	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[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]
rs2972419	0.80[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs34509769	0.93[EUR][1000 genomes]
rs3764453	0.96[ASN][1000 genomes]
rs4358532	0.91[ASN][1000 genomes]
rs4642376	1.00[CEU][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs4866781	0.93[ASN][1000 genomes]
rs4866782	0.93[ASN][1000 genomes]
rs4866788	0.89[ASN][1000 genomes]
rs4866795	0.98[ASN][1000 genomes]
rs4866890	0.99[EUR][1000 genomes]
rs4866896	0.98[ASN][1000 genomes]
rs4866901	0.98[ASN][1000 genomes]
rs4866919	0.93[ASN][1000 genomes]
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]
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	0.83[ASW][hapmap];0.89[CEU][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs906817	0.98[ASN][1000 genomes]
rs9686286	0.98[EUR][1000 genomes]
rs9686537	0.96[ASN][1000 genomes]
rs9687863	0.93[ASN][1000 genomes]
rs974051	0.80[CEU][hapmap];0.90[EUR][1000 genomes]
rs979233	0.96[ASN][1000 genomes]
rs991592	0.96[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
rs1876790	GHR	cis	parietal	SCAN
rs1876790	TTC33	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42421600-42423000	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr5:42422000-42423000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:42422000-42423000	Enhancers	Colon Smooth Muscle	Colon
4	chr5:42422000-42423000	Enhancers	Fetal Lung	lung
5	chr5:42422000-42423000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr5:42422200-42423000	Enhancers	Fetal Stomach	stomach
7	chr5:42422400-42423000	Enhancers	Adipose Nuclei	Adipose
8	chr5:42422400-42423000	Enhancers	Rectal Smooth Muscle	rectum
9	chr5:42422400-42423200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:42422400-42423200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:42422600-42423000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:42422600-42423000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:42422600-42423000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr5:42422800-42423000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:42422800-42423000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:42422800-42423000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:42422800-42423000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:42422800-42423000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:42422800-42423000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:42422800-42423000	Enhancers	Liver	Liver
21	chr5:42422800-42423000	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:42422800-42423000	Enhancers	Brain Hippocampus Middle	brain
23	chr5:42422800-42423000	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:42422800-42423000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:42422800-42423000	Enhancers	Fetal Heart	heart
26	chr5:42422800-42423000	Enhancers	Fetal Intestine Large	intestine
27	chr5:42422800-42423000	Enhancers	Fetal Kidney	kidney
28	chr5:42422800-42423000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr5:42422800-42423000	Enhancers	Stomach Smooth Muscle	stomach
30	chr5:42422800-42423000	Enhancers	HMEC	breast
31	chr5:42422800-42423000	Enhancers	HSMM	muscle
32	chr5:42422800-42423000	Enhancers	NH-A	brain
33	chr5:42422800-42423000	Enhancers	NHDF-Ad	bronchial
34	chr5:42422800-42423000	Enhancers	NHEK	skin

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