Variant report

Variant	rs2838989
Chromosome Location	chr21:47170084-47170085
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	chr21:47061926..47064777-chr21:47168199..47170677,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL6A1-3	chr21:47170041-47170255	NONHSAT082983
2	lnc-COL6A1-3	chr21:47169787-47170389	NONHSAT082987

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1014446	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1029014	0.91[ASN][1000 genomes]
rs11089024	0.92[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs12151963	0.91[ASN][1000 genomes]
rs12329841	0.87[EUR][1000 genomes]
rs12329855	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12481867	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12481913	0.86[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	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12482648	0.91[EUR][1000 genomes];0.88[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];0.86[EUR][1000 genomes]
rs12483701	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13051489	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1467758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17004799	0.91[ASN][1000 genomes]
rs17351433	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1964928	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1989537	0.86[ASN][1000 genomes]
rs2065334	1.00[JPT][hapmap]
rs2094888	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2150460	0.91[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2183601	0.86[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];0.88[ASN][1000 genomes]
rs2838974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2838976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2838978	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838981	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2838983	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838985	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838988	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838990	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838993	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2838994	1.00[ASW][hapmap];0.87[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];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838995	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838996	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2838997	0.86[ASN][1000 genomes]
rs2838998	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838999	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839000	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839001	0.82[ASN][1000 genomes]
rs2839002	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839003	0.86[EUR][1000 genomes]
rs2839004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2839005	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2839009	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs2839013	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2839014	0.86[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	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28625750	0.85[AMR][1000 genomes];0.91[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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788211	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs3788216	0.86[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	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs3920695	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.88[ASN][1000 genomes]
rs4347938	0.88[ASN][1000 genomes]
rs4434082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4818795	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4818797	0.91[ASN][1000 genomes]
rs4818798	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4818801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4819144	0.91[ASN][1000 genomes]
rs4819151	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4819152	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4819156	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4819157	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs55707606	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55780126	0.85[EUR][1000 genomes]
rs55875620	0.85[EUR][1000 genomes]
rs55912508	0.91[ASN][1000 genomes]
rs55923134	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55957843	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56012600	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56036552	0.86[EUR][1000 genomes]
rs56213918	0.86[ASN][1000 genomes]
rs56256701	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56288252	0.88[ASN][1000 genomes]
rs56300316	0.91[ASN][1000 genomes]
rs56323347	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56347571	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56378934	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57328058	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57501220	0.88[ASN][1000 genomes]
rs57990579	0.83[ASN][1000 genomes]
rs58925015	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58952758	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59398815	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59785950	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60604183	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61100346	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61329313	0.91[ASN][1000 genomes]
rs62213277	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62213555	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62214592	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214596	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214597	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214599	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62214604	0.86[EUR][1000 genomes]
rs62215031	0.88[ASN][1000 genomes]
rs62215035	0.88[ASN][1000 genomes]
rs62215040	0.88[ASN][1000 genomes]
rs62215047	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62215048	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs66552772	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66991496	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67565220	0.86[ASN][1000 genomes]
rs725358	0.91[ASN][1000 genomes]
rs7276632	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7279909	0.91[ASN][1000 genomes]
rs7280560	0.91[ASN][1000 genomes]
rs7283803	0.88[ASN][1000 genomes]
rs767137	0.91[ASN][1000 genomes]
rs8127369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8127428	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs8127809	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8128722	0.80[ASN][1000 genomes]
rs8133966	0.91[ASN][1000 genomes]
rs882669	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs914241	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]
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];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9637169	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9637205	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637206	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637208	0.86[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9647229	0.91[ASN][1000 genomes]
rs9647230	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9975404	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9976200	0.91[ASN][1000 genomes]
rs9976878	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9977309	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9977908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9978078	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9978158	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9978740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9978882	0.88[ASN][1000 genomes]
rs9981586	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2838989	COL6A1	cis	parietal	SCAN
rs2838989	PCBP3	cis	Heart Left Ventricle	GTEx
rs2838989	PCBP3	cis	Muscle Skeletal	GTEx
rs2838989	PCBP3	cis	cerebellum	SCAN
rs2838989	COL6A1	cis	cerebellum	SCAN
rs2838989	TRPM2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47165800-47171000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr21:47166000-47171400	Weak transcription	Gastric	stomach
3	chr21:47166200-47174400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr21:47166200-47176800	Weak transcription	Dnd41	blood
5	chr21:47166200-47194400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr21:47167600-47170200	Genic enhancers	Fetal Thymus	thymus
7	chr21:47167800-47176200	Weak transcription	NH-A	brain
8	chr21:47168000-47170600	Weak transcription	Fetal Brain Female	brain
9	chr21:47168200-47170200	Strong transcription	Spleen	Spleen
10	chr21:47168400-47171800	Weak transcription	Adipose Nuclei	Adipose
11	chr21:47168400-47172000	Weak transcription	Brain Anterior Caudate	brain
12	chr21:47168400-47172400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr21:47168600-47170600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr21:47168600-47187000	Weak transcription	NHDF-Ad	bronchial
15	chr21:47168800-47172400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr21:47168800-47183000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:47169000-47171000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr21:47169000-47176000	Weak transcription	Primary T cells from cord blood	blood
19	chr21:47169200-47174200	Weak transcription	HSMMtube	muscle
20	chr21:47169400-47175800	Weak transcription	HSMM	muscle
21	chr21:47169600-47171800	Strong transcription	Thymus	Thymus
22	chr21:47169800-47172000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:47169800-47172400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr21:47170000-47179800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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