Variant report

Variant	rs914241
Chromosome Location	chr21:47182965-47182966
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	chr21:47180995..47184771-chr21:47188316..47191087,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC19A1-9	chr21:47179718-47183672	NONHSAT082989

Variant related genes	Relation type
ENSG00000267883	Chromatin interaction

Extended variants
information (count: 169 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1029014	0.86[ASN][1000 genomes]
rs11089024	0.92[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs12151963	0.86[ASN][1000 genomes]
rs12329841	0.88[EUR][1000 genomes]
rs12329855	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12381207	0.81[ASN][1000 genomes]
rs12481867	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12481913	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12482094	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs12482377	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12482405	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12482648	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12482750	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs12482853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12483701	0.86[ASN][1000 genomes]
rs13051489	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1467758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17004799	0.86[ASN][1000 genomes]
rs17351433	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1964928	0.86[ASN][1000 genomes]
rs1989537	0.82[ASN][1000 genomes]
rs2065334	1.00[JPT][hapmap]
rs2094888	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2150460	0.86[ASN][1000 genomes]
rs2183595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183596	1.00[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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183601	0.81[ASN][1000 genomes]
rs2838973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs2838974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838978	0.86[ASN][1000 genomes]
rs2838981	0.86[ASN][1000 genomes]
rs2838982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2838983	0.86[ASN][1000 genomes]
rs2838985	0.86[ASN][1000 genomes]
rs2838988	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2838989	1.00[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];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838990	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838993	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838994	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838995	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838996	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838997	0.91[ASN][1000 genomes]
rs2838998	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838999	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2839000	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2839001	0.86[ASN][1000 genomes]
rs2839002	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2839003	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2839013	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2839014	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2839026	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839029	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839032	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28583990	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28625750	0.86[ASN][1000 genomes]
rs3367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35781238	0.84[ASN][1000 genomes]
rs3788211	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788216	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3788220	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788224	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs3788227	0.85[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs3920695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs4347938	0.84[ASN][1000 genomes]
rs4434082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs4818795	0.84[ASN][1000 genomes]
rs4818797	0.86[ASN][1000 genomes]
rs4818798	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4819134	0.81[ASN][1000 genomes]
rs4819144	0.86[ASN][1000 genomes]
rs4819151	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4819152	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4819156	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4819157	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs55707606	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55780126	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55875620	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55912508	0.86[ASN][1000 genomes]
rs55923134	0.86[ASN][1000 genomes]
rs55957843	0.86[ASN][1000 genomes]
rs56012600	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56036552	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56213918	0.81[ASN][1000 genomes]
rs56256701	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56288252	0.84[ASN][1000 genomes]
rs56300316	0.86[ASN][1000 genomes]
rs56323347	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56347571	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56378934	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57057834	0.83[ASN][1000 genomes]
rs57282159	0.83[ASN][1000 genomes]
rs57328058	0.86[ASN][1000 genomes]
rs57501220	0.84[ASN][1000 genomes]
rs58925015	0.86[ASN][1000 genomes]
rs58952758	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59398815	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59785950	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60604183	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60988006	0.83[ASN][1000 genomes]
rs61100346	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61329313	0.86[ASN][1000 genomes]
rs61540945	0.81[ASN][1000 genomes]
rs62213277	0.84[ASN][1000 genomes]
rs62213555	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62214592	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62214596	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62214597	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62214599	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62214604	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62215031	0.84[ASN][1000 genomes]
rs62215035	0.84[ASN][1000 genomes]
rs62215040	0.84[ASN][1000 genomes]
rs62215047	0.86[ASN][1000 genomes]
rs62215048	0.86[ASN][1000 genomes]
rs62216072	0.81[ASN][1000 genomes]
rs66552772	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66991496	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67222545	0.81[ASN][1000 genomes]
rs67565220	0.81[ASN][1000 genomes]
rs725358	0.86[ASN][1000 genomes]
rs7276632	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7279909	0.86[ASN][1000 genomes]
rs7280055	0.81[ASN][1000 genomes]
rs7280560	0.86[ASN][1000 genomes]
rs7283803	0.84[ASN][1000 genomes]
rs7410008	0.83[ASN][1000 genomes]
rs744506	0.83[ASN][1000 genomes]
rs767137	0.86[ASN][1000 genomes]
rs8127369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8127428	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs8127809	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8128722	0.85[ASN][1000 genomes]
rs8133966	0.86[ASN][1000 genomes]
rs882669	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs9306139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs9637169	0.86[ASN][1000 genomes]
rs9637205	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9637206	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9637208	0.85[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9647229	0.86[ASN][1000 genomes]
rs9647230	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964975	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs9974491	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975404	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9976200	0.86[ASN][1000 genomes]
rs9976878	0.84[ASN][1000 genomes]
rs9977309	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9977908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9978078	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978158	0.86[ASN][1000 genomes]
rs9978740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9978882	0.84[ASN][1000 genomes]
rs9981586	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs914241	COL6A1	cis	parietal	SCAN
rs914241	PCBP3	cis	Muscle Skeletal	GTEx
rs914241	COL6A1	cis	cerebellum	SCAN
rs914241	TRPM2	cis	cerebellum	SCAN
rs914241	PCBP3	cis	Heart Left Ventricle	GTEx
rs914241	PCBP3	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47166200-47194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr21:47168600-47187000	Weak transcription	NHDF-Ad	bronchial
3	chr21:47168800-47183000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr21:47170200-47188800	Weak transcription	Spleen	Spleen
5	chr21:47170800-47188200	Weak transcription	Right Atrium	heart
6	chr21:47171800-47186600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr21:47175600-47186000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr21:47177200-47187400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr21:47180000-47186600	Strong transcription	Thymus	Thymus
10	chr21:47180400-47187000	Weak transcription	HSMMtube	muscle
11	chr21:47180600-47186800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr21:47181600-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:47182000-47186600	Weak transcription	Primary T cells from cord blood	blood
14	chr21:47182400-47186400	Strong transcription	Fetal Thymus	thymus
15	chr21:47182800-47183000	Enhancers	Brain Germinal Matrix	brain
16	chr21:47182800-47183000	Weak transcription	NH-A	brain
17	chr21:47182800-47183400	Bivalent Enhancer	Fetal Stomach	stomach

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