Variant report

Variant	rs2101064
Chromosome Location	chr3:43563332-43563333
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43561682..43564008-chr3:43566171..43568644,2	MCF-7	breast:
2	chr3:43538412..43541207-chr3:43562401..43564884,2	K562	blood:
3	chr3:43559073..43563510-chr3:43563874..43567670,4	K562	blood:
4	chr3:43562292..43564577-chr3:43568743..43570815,2	K562	blood:
5	chr3:43562365..43565525-chr3:43571764..43575100,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1013758	0.88[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs1038202	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10461013	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs10461015	0.89[EUR][1000 genomes]
rs11130004	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130005	0.87[CEU][hapmap];0.96[EUR][1000 genomes]
rs11715896	0.82[CEU][hapmap]
rs12374079	0.86[EUR][1000 genomes]
rs12486736	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492694	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12638282	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13066902	0.83[EUR][1000 genomes]
rs13319147	0.91[EUR][1000 genomes]
rs1351631	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1384435	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564434	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17030517	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs17408925	0.87[EUR][1000 genomes]
rs1842806	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1842807	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1975997	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054553	0.86[EUR][1000 genomes]
rs2054554	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs2127725	0.82[EUR][1000 genomes]
rs34279519	0.84[EUR][1000 genomes]
rs3772160	0.88[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs3772165	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs3772167	0.82[CEU][hapmap]
rs3821381	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs3902207	0.88[EUR][1000 genomes]
rs4128530	0.83[CEU][hapmap]
rs4264704	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4407383	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4505672	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4547674	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4561805	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682690	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs61102363	0.94[EUR][1000 genomes]
rs6441786	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs6763321	0.86[EUR][1000 genomes]
rs6769576	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737516	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616708	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7621271	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs7621298	0.88[GIH][hapmap]
rs9311340	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311341	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs9809643	0.88[CEU][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs9814737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815196	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824990	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9826275	0.85[EUR][1000 genomes]
rs9829067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830697	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834786	0.89[EUR][1000 genomes]
rs9835664	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9835793	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845142	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9851894	0.82[EUR][1000 genomes]
rs9852783	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9862259	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs9873316	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9878330	0.86[EUR][1000 genomes]
rs9881028	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	nsv428738	chr3:43491435-43651168	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv2763720	chr3:43551038-43575884	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2101064	PTH1R	cis	parietal	SCAN
rs2101064	SNRK	cis	cerebellum	SCAN
rs2101064	RPL14	cis	parietal	SCAN
rs2101064	MRPS18A	trans	cerebellum	SCAN
rs2101064	NKTR	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43539200-43575000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:43540000-43582000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:43540200-43564600	Weak transcription	NHEK	skin
4	chr3:43540200-43602200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:43542800-43588800	Weak transcription	Left Ventricle	heart
6	chr3:43544000-43617600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:43547200-43567200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:43547600-43595800	Weak transcription	Fetal Stomach	stomach
9	chr3:43551000-43577800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:43552000-43564200	Weak transcription	Gastric	stomach
11	chr3:43553000-43601600	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:43553600-43595800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:43554000-43579000	Weak transcription	Fetal Brain Male	brain
14	chr3:43554800-43564400	Weak transcription	Osteobl	bone
15	chr3:43554800-43564600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:43554800-43564600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:43554800-43565200	Weak transcription	NHDF-Ad	bronchial
18	chr3:43554800-43565400	Weak transcription	NHLF	lung
19	chr3:43554800-43573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:43554800-43589400	Weak transcription	HSMMtube	muscle
21	chr3:43555400-43567800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:43556200-43624800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:43557000-43577200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:43558600-43564200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:43558600-43625600	Weak transcription	Lung	lung
26	chr3:43559400-43565000	Weak transcription	Aorta	Aorta
27	chr3:43559600-43564000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:43559600-43568400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:43559600-43569200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:43559800-43564600	Weak transcription	NH-A	brain
31	chr3:43560600-43564600	Weak transcription	HMEC	breast
32	chr3:43560800-43563400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:43560800-43568400	Weak transcription	Colonic Mucosa	Colon
34	chr3:43560800-43618000	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:43561000-43567600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:43561200-43565000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:43561200-43565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:43561200-43601200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:43561400-43600400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:43561600-43566400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:43561600-43569400	Weak transcription	Adipose Nuclei	Adipose
42	chr3:43561600-43570400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:43561600-43588800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:43561600-43589000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:43561600-43590600	Weak transcription	Ovary	ovary
46	chr3:43561600-43601000	Weak transcription	Pancreas	Pancrea
47	chr3:43561800-43563400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:43561800-43563600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:43561800-43564000	Weak transcription	K562	blood
50	chr3:43561800-43564200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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