Variant report

Variant	rs9653780
Chromosome Location	chr21:47303774-47303775
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	chr21:47298754..47301234-chr21:47302328..47305027,3	K562	blood:
2	chr21:47292095..47293643-chr21:47302560..47304735,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1059010	1.00[ASN][1000 genomes]
rs10854474	1.00[ASN][1000 genomes]
rs10854475	1.00[ASN][1000 genomes]
rs11089025	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089028	0.83[EUR][1000 genomes]
rs11701693	1.00[ASN][1000 genomes]
rs1625244	1.00[ASN][1000 genomes]
rs1736424	1.00[ASN][1000 genomes]
rs1783076	1.00[ASN][1000 genomes]
rs2014421	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026286	1.00[ASN][1000 genomes]
rs2150453	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150454	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2210290	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2277812	1.00[ASN][1000 genomes]
rs2330327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776402	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2839020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839035	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839039	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs2839041	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2839050	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs2839054	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs34495634	1.00[ASN][1000 genomes]
rs34990419	1.00[ASN][1000 genomes]
rs369245	1.00[ASN][1000 genomes]
rs371587	1.00[ASN][1000 genomes]
rs373267	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs374331	1.00[ASN][1000 genomes]
rs375254	1.00[ASN][1000 genomes]
rs375971	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs377213	1.00[ASN][1000 genomes]
rs3788217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380120	1.00[ASN][1000 genomes]
rs382195	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs382303	1.00[ASN][1000 genomes]
rs402039	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs402355	1.00[ASN][1000 genomes]
rs403192	1.00[ASN][1000 genomes]
rs407651	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs410902	1.00[ASN][1000 genomes]
rs413246	1.00[ASN][1000 genomes]
rs413517	1.00[ASN][1000 genomes]
rs420386	1.00[ASN][1000 genomes]
rs425232	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs432338	1.00[ASN][1000 genomes]
rs4369958	1.00[ASN][1000 genomes]
rs439145	1.00[ASN][1000 genomes]
rs442953	1.00[ASN][1000 genomes]
rs451920	1.00[ASN][1000 genomes]
rs452797	1.00[ASN][1000 genomes]
rs454268	1.00[ASN][1000 genomes]
rs4818804	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819143	1.00[ASN][1000 genomes]
rs4819159	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56695931	1.00[ASN][1000 genomes]
rs6518257	1.00[ASN][1000 genomes]
rs6518258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518259	1.00[ASN][1000 genomes]
rs71324446	1.00[ASN][1000 genomes]
rs7276114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277632	1.00[ASN][1000 genomes]
rs7279887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280054	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283688	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159604	1.00[ASN][1000 genomes]
rs7410101	1.00[ASN][1000 genomes]
rs7410105	1.00[ASN][1000 genomes]
rs753092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760436	0.91[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8131193	1.00[CHB][hapmap]
rs8133932	1.00[ASN][1000 genomes]
rs9637207	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9653791	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989650	1.00[ASN][1000 genomes]
rs9976042	1.00[ASN][1000 genomes]
rs9984663	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
15	nsv914080	chr21:47265786-47311686	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv914081	chr21:47265786-47320805	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
18	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
19	nsv914084	chr21:47288453-47326666	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	esv14817	chr21:47293464-47303825	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
22	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9653780	ITGB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47295600-47309200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:47298000-47306600	Weak transcription	NH-A	brain
3	chr21:47300400-47305400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr21:47300400-47305800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr21:47300600-47306000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr21:47300800-47304000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr21:47300800-47305600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr21:47300800-47305600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr21:47300800-47306200	Weak transcription	Right Ventricle	heart
10	chr21:47301000-47303800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr21:47301000-47304000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr21:47301000-47305000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr21:47301000-47305000	Weak transcription	Thymus	Thymus
14	chr21:47301000-47305400	Weak transcription	Spleen	Spleen
15	chr21:47301000-47305600	Weak transcription	Brain Angular Gyrus	brain
16	chr21:47301000-47306400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:47301000-47306400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:47301000-47306400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:47301000-47306400	Weak transcription	Brain Substantia Nigra	brain
20	chr21:47301000-47306800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr21:47301000-47307000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:47301200-47304400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr21:47301200-47304400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr21:47301200-47304400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr21:47301200-47306200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr21:47301200-47306600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr21:47301400-47304400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr21:47301400-47305000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr21:47301400-47306400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:47301400-47306400	Weak transcription	NHEK	skin
31	chr21:47301600-47304400	Weak transcription	Primary T cells from cord blood	blood
32	chr21:47301600-47304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr21:47301600-47305000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr21:47301600-47305000	Weak transcription	Fetal Thymus	thymus
35	chr21:47301600-47305600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr21:47301600-47305800	Weak transcription	HMEC	breast
37	chr21:47301800-47304400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr21:47302000-47303800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr21:47302000-47304200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr21:47302200-47305800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr21:47302200-47305800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr21:47302400-47304400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr21:47302600-47303800	Enhancers	HSMMtube	muscle
44	chr21:47302800-47304000	Enhancers	HSMM	muscle
45	chr21:47302800-47306600	Weak transcription	Brain Germinal Matrix	brain
46	chr21:47303000-47304400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr21:47303000-47305800	Weak transcription	Brain Hippocampus Middle	brain
48	chr21:47303000-47306400	Weak transcription	Fetal Muscle Leg	muscle
49	chr21:47303400-47304400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr21:47303600-47303800	Enhancers	Primary T helper cells PMA-I stimulated	--

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