Variant report

Variant	rs9311340
Chromosome Location	chr3:43517423-43517424
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43513364..43515797-chr3:43516970..43520090,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251811	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1013758	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs1038202	0.92[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	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130005	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11715896	0.92[CEU][hapmap]
rs12374079	0.82[EUR][1000 genomes]
rs12486736	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12492694	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12638282	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13066902	0.87[EUR][1000 genomes]
rs13319147	0.87[EUR][1000 genomes]
rs1351631	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs1384435	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];1.00[MKK][hapmap];1.00[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]
rs1482651	0.81[CEU][hapmap]
rs1564434	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]
rs17030517	0.92[CEU][hapmap]
rs17408925	0.83[EUR][1000 genomes]
rs1842806	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1842807	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1975997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2054553	0.82[EUR][1000 genomes]
rs2054554	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2101064	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]
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	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs3772167	0.92[CEU][hapmap]
rs3821381	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs3902207	0.84[EUR][1000 genomes]
rs4128530	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4264704	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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];0.86[ASN][1000 genomes]
rs4505672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];0.90[ASN][1000 genomes]
rs4561805	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4682690	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs4682691	0.81[CEU][hapmap]
rs61102363	0.98[EUR][1000 genomes]
rs6441786	0.92[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];0.87[ASN][1000 genomes]
rs6793392	0.88[GIH][hapmap]
rs737516	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];1.00[MKK][hapmap];1.00[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]
rs7616708	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7621271	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7621298	0.90[GIH][hapmap]
rs9311341	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9809643	0.83[ASW][hapmap];0.92[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs9814737	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9815196	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs9824990	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9826275	0.81[EUR][1000 genomes]
rs9829067	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834786	0.85[EUR][1000 genomes]
rs9835664	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9835793	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845142	0.88[EUR][1000 genomes];0.87[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[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878330	0.82[EUR][1000 genomes]
rs9881028	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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
rs9311340	MRPS18A	trans	cerebellum	SCAN
rs9311340	RPL14	cis	parietal	SCAN
rs9311340	SNRK	cis	cerebellum	SCAN
rs9311340	PTH1R	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43473400-43541400	Weak transcription	Aorta	Aorta
2	chr3:43497000-43539400	Weak transcription	HSMM	muscle
3	chr3:43497200-43519600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:43497200-43520000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:43497200-43532600	Weak transcription	K562	blood
6	chr3:43504800-43553400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:43505400-43518800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:43506600-43522800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:43508600-43521800	Weak transcription	HSMMtube	muscle
10	chr3:43509400-43517800	Weak transcription	Primary T cells from cord blood	blood
11	chr3:43509600-43517600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:43509800-43518000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:43510000-43517800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:43510000-43519000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:43510000-43521200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:43510000-43521600	Weak transcription	Brain Substantia Nigra	brain
17	chr3:43510800-43519200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:43512400-43517800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:43513000-43524600	Weak transcription	Psoas Muscle	Psoas
20	chr3:43515000-43519600	Weak transcription	Adipose Nuclei	Adipose
21	chr3:43515000-43526400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:43515000-43532400	Weak transcription	Pancreas	Pancrea
23	chr3:43515400-43519200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:43515600-43521200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:43515600-43521800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:43515600-43523400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:43515800-43519200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:43516000-43526600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:43516400-43517600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:43516600-43517800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:43516600-43522200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:43517200-43517600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:43517400-43520000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:43517400-43521600	Enhancers	Primary T helper cells fromperipheralblood	blood

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