Variant report

Variant	rs1564434
Chromosome Location	chr3:43540052-43540053
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	chr3:43538412..43541207-chr3:43562401..43564884,2	K562	blood:
2	chr3:43537054..43539250-chr3:43539442..43541239,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1013758	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs1038202	0.85[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs10461013	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs10461015	0.85[EUR][1000 genomes]
rs11130004	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130005	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11715896	0.85[CEU][hapmap]
rs12374079	0.82[EUR][1000 genomes]
rs12486736	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492694	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12638282	0.85[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13066902	0.87[EUR][1000 genomes]
rs13319147	0.87[EUR][1000 genomes]
rs1351631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1384435	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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	0.85[CEU][hapmap]
rs17408925	0.83[EUR][1000 genomes]
rs1842806	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1842807	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1975997	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054553	0.82[EUR][1000 genomes]
rs2054554	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2101064	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]
rs34279519	0.88[EUR][1000 genomes]
rs3772160	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs3772165	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772167	0.85[CEU][hapmap]
rs3821381	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs3902207	0.84[EUR][1000 genomes]
rs4128530	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4264704	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407383	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4505672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547674	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4561805	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682690	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs61102363	0.98[EUR][1000 genomes]
rs6441786	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs6763321	0.82[EUR][1000 genomes]
rs6769576	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737516	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs7616708	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7621271	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7621298	0.90[GIH][hapmap]
rs9311340	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9311341	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9809643	0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs9814737	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9815196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9824990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9826275	0.81[EUR][1000 genomes]
rs9829067	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834786	0.85[EUR][1000 genomes]
rs9835664	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9835793	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845142	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9852783	0.91[GIH][hapmap];0.91[TSI][hapmap]
rs9862259	0.89[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs9873316	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878330	0.82[EUR][1000 genomes]
rs9881028	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1564434	RPL14	cis	parietal	SCAN
rs1564434	SNRK	cis	cerebellum	SCAN
rs1564434	PTH1R	cis	parietal	SCAN
rs1564434	MRPS18A	trans	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43473400-43541400	Weak transcription	Aorta	Aorta
2	chr3:43504800-43553400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:43526000-43560800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:43527200-43560200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:43531200-43542600	Weak transcription	Psoas Muscle	Psoas
6	chr3:43532400-43540800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:43532600-43540800	Weak transcription	Spleen	Spleen
8	chr3:43533000-43553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:43533200-43544800	Weak transcription	K562	blood
10	chr3:43538000-43540800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:43538200-43540200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:43538200-43540200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:43538200-43540200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:43538200-43540200	Enhancers	HMEC	breast
15	chr3:43538200-43540200	Enhancers	NHEK	skin
16	chr3:43538400-43541600	Enhancers	Adipose Nuclei	Adipose
17	chr3:43538400-43545200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:43538600-43540400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:43538600-43540400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr3:43539000-43540600	Enhancers	Lung	lung
21	chr3:43539000-43540800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:43539000-43542800	Enhancers	Left Ventricle	heart
23	chr3:43539000-43545400	Enhancers	HUVEC	blood vessel
24	chr3:43539200-43540200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:43539200-43575000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:43539400-43540200	Enhancers	HSMM	muscle
27	chr3:43539600-43540600	Enhancers	Right Ventricle	heart
28	chr3:43539600-43541000	Enhancers	Right Atrium	heart
29	chr3:43539600-43541800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:43539600-43541800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:43539600-43558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:43539800-43540200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:43539800-43540200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:43539800-43540600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr3:43539800-43543800	Weak transcription	NH-A	brain
36	chr3:43539800-43544400	Enhancers	Primary T cells fromperipheralblood	blood
37	chr3:43539800-43544800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:43539800-43544800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:43539800-43545200	Enhancers	Primary T cells from cord blood	blood
40	chr3:43539800-43546400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:43539800-43553800	Weak transcription	HSMMtube	muscle
42	chr3:43540000-43540200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:43540000-43541600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr3:43540000-43542600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:43540000-43544800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:43540000-43546200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:43540000-43546600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:43540000-43548800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:43540000-43554200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:43540000-43554400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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