Variant report

Variant	rs7281757
Chromosome Location	chr21:46636161-46636162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46534502..46536966-chr21:46634899..46637036,2	K562	blood:
2	chr21:46620976..46623601-chr21:46635556..46637129,2	MCF-7	breast:
3	chr21:46617207..46619731-chr21:46635917..46638327,2	K562	blood:

Variant related genes	Relation type
ENSG00000267857	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11088982	0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11088983	0.89[CHB][hapmap]
rs12185823	0.88[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13047803	0.88[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1537121	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1556317	0.83[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2150439	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2253763	0.85[CHB][hapmap];0.83[AMR][1000 genomes]
rs2838791	0.82[JPT][hapmap]
rs2838797	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2838803	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2838807	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28782181	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs372766	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs377524	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs3788180	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs381466	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs386762	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs422720	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs434492	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs446158	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes]
rs4818766	0.81[CEU][hapmap]
rs4819030	0.88[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4819031	0.91[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6518214	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7281416	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8126717	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8126895	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8128889	0.84[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8130224	0.84[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8133307	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8134789	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs914210	0.80[CHB][hapmap]
rs983749	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9974232	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv587841	chr21:46619840-46647078	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7281757	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46589000-46646000	Weak transcription	Colonic Mucosa	Colon
2	chr21:46606800-46640800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr21:46610000-46644800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr21:46610400-46641000	Weak transcription	Brain Germinal Matrix	brain
5	chr21:46610400-46641800	Weak transcription	HepG2	liver
6	chr21:46610800-46640200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr21:46610800-46641000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr21:46610800-46641200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:46610800-46647800	Weak transcription	Brain Angular Gyrus	brain
10	chr21:46611000-46639600	Weak transcription	Fetal Brain Male	brain
11	chr21:46611000-46639600	Weak transcription	Gastric	stomach
12	chr21:46611000-46644600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr21:46611000-46645000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr21:46621800-46640400	Weak transcription	Fetal Brain Female	brain
15	chr21:46622000-46640600	Weak transcription	Brain Substantia Nigra	brain
16	chr21:46622800-46640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr21:46624600-46638600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr21:46625000-46645000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr21:46625200-46640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr21:46625600-46639600	Weak transcription	Placenta	Placenta
21	chr21:46625600-46640800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr21:46626000-46636600	Weak transcription	Brain Anterior Caudate	brain
23	chr21:46628200-46639600	Weak transcription	NHEK	skin
24	chr21:46628600-46638000	Weak transcription	HMEC	breast
25	chr21:46628600-46640200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr21:46628600-46640400	Weak transcription	Esophagus	oesophagus
27	chr21:46628600-46644200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr21:46628800-46644600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr21:46628800-46644800	Strong transcription	HSMM	muscle
30	chr21:46629600-46638400	Weak transcription	Osteobl	bone
31	chr21:46629600-46645400	Weak transcription	NHLF	lung
32	chr21:46630800-46640200	Weak transcription	Pancreas	Pancrea
33	chr21:46630800-46640400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr21:46631000-46640200	Weak transcription	Fetal Intestine Small	intestine
35	chr21:46631000-46640600	Weak transcription	Thymus	Thymus
36	chr21:46631000-46640800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr21:46631000-46641000	Weak transcription	Brain Hippocampus Middle	brain
38	chr21:46631200-46638400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr21:46631200-46640200	Weak transcription	Right Ventricle	heart
40	chr21:46631400-46636600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr21:46631400-46637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr21:46631400-46638400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr21:46632000-46638400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr21:46632200-46638600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr21:46632400-46636400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr21:46632400-46637000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr21:46632400-46638200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr21:46632400-46639600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr21:46632600-46636600	Weak transcription	Dnd41	blood
50	chr21:46632600-46637000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links