Variant report

Variant	rs748559
Chromosome Location	chr21:46647582-46647583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46646544..46648197-chr21:46659492..46661495,2	MCF-7	breast:
2	chr21:46644635..46649401-chr21:46653595..46657283,5	MCF-7	breast:
3	chr21:46495879..46498410-chr21:46645680..46647627,2	K562	blood:
4	chr21:46617772..46620872-chr21:46645062..46648136,3	K562	blood:
5	chr21:46642556..46644415-chr21:46646338..46649203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182586	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1106627	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12329821	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17004755	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17004756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17004757	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17004759	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28531382	0.91[ASN][1000 genomes]
rs2877017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3753018	0.84[CHB][hapmap]
rs4592938	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73369026	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs748557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9306121	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9306122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv1059779	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	nsv544485	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv1059805	chr21:46618210-46736943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv913999	chr21:46636844-46765251	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv587842	chr21:46641017-46670752	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
19	nsv914000	chr21:46647078-46765251	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
20	nsv914001	chr21:46647078-46944113	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs748559	PGAM2	trans	brain	seeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46610800-46647800	Weak transcription	Brain Angular Gyrus	brain
2	chr21:46637800-46668600	Weak transcription	Right Atrium	heart
3	chr21:46639800-46648000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr21:46641000-46648000	Weak transcription	Fetal Brain Male	brain
5	chr21:46641600-46648400	Weak transcription	Brain Substantia Nigra	brain
6	chr21:46642000-46648800	Weak transcription	Primary B cells from cord blood	blood
7	chr21:46642200-46648000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr21:46642400-46649200	Weak transcription	Fetal Intestine Small	intestine
9	chr21:46642800-46647800	Weak transcription	Brain Hippocampus Middle	brain
10	chr21:46643600-46649600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr21:46643800-46647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:46643800-46647800	Weak transcription	Brain Anterior Caudate	brain
13	chr21:46643800-46648000	Weak transcription	Esophagus	oesophagus
14	chr21:46643800-46648800	Weak transcription	Left Ventricle	heart
15	chr21:46643800-46664600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:46644000-46647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr21:46644000-46647800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr21:46644000-46647800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:46644000-46647800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr21:46644000-46648000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr21:46644000-46648000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr21:46644000-46648200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr21:46644000-46652200	Weak transcription	Pancreas	Pancrea
24	chr21:46644200-46647600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr21:46644200-46648000	Weak transcription	Colon Smooth Muscle	Colon
26	chr21:46644200-46648400	Weak transcription	Fetal Muscle Leg	muscle
27	chr21:46644200-46648800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr21:46644200-46649000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr21:46644200-46649200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr21:46644400-46648400	Weak transcription	Lung	lung
31	chr21:46644400-46648600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr21:46644400-46649200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr21:46644600-46648400	Weak transcription	Aorta	Aorta
34	chr21:46644600-46648800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr21:46644600-46649000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr21:46645000-46649000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr21:46645000-46649200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr21:46645000-46649600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr21:46645400-46649400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr21:46645600-46647600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr21:46646000-46648200	Weak transcription	Hela-S3	cervix
42	chr21:46646400-46648200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr21:46646400-46649000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr21:46646400-46649200	Enhancers	HMEC	breast
45	chr21:46646400-46649200	Enhancers	HSMMtube	muscle
46	chr21:46646400-46649600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr21:46646600-46647600	Enhancers	NH-A	brain
48	chr21:46646600-46648200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr21:46646600-46648400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr21:46646600-46649200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links