Variant report

Variant	rs3788154
Chromosome Location	chr21:46501346-46501347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46425775..46427394-chr21:46498678..46501508,2	MCF-7	breast:
2	chr21:46500190..46501705-chr21:46518779..46520799,2	K562	blood:
3	chr21:46499894..46505152-chr21:46506062..46510299,9	MCF-7	breast:
4	chr21:46499575..46502481-chr21:46547014..46549747,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12482868	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12482952	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483115	0.87[ASN][1000 genomes]
rs12483279	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12483312	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483758	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556316	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17004734	0.96[ASN][1000 genomes]
rs17004739	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838774	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838776	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838786	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838789	0.88[ASN][1000 genomes]
rs3178603	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs367228	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs372173	0.80[ASN][1000 genomes]
rs3746976	0.83[EUR][1000 genomes]
rs3788155	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788156	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3788163	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs386528	0.87[ASN][1000 genomes]
rs391834	0.80[ASN][1000 genomes]
rs406551	0.86[ASN][1000 genomes]
rs421643	0.87[ASN][1000 genomes]
rs423726	0.87[ASN][1000 genomes]
rs428870	0.85[ASN][1000 genomes]
rs431529	0.87[ASN][1000 genomes]
rs431666	0.87[ASN][1000 genomes]
rs431775	0.87[ASN][1000 genomes]
rs437286	0.80[ASN][1000 genomes]
rs439884	0.87[ASN][1000 genomes]
rs442380	0.87[ASN][1000 genomes]
rs447656	0.87[ASN][1000 genomes]
rs454052	0.80[ASN][1000 genomes]
rs7275205	1.00[ASN][1000 genomes]
rs7275931	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7281718	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283619	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs731248	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8127577	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8129934	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8132454	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8132752	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8134889	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs870145	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870350	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870351	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
3	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46495600-46501400	Weak transcription	Gastric	stomach
2	chr21:46495800-46501400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:46495800-46502600	Weak transcription	Colonic Mucosa	Colon
4	chr21:46495800-46506000	Weak transcription	Pancreas	Pancrea
5	chr21:46496200-46506600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr21:46496200-46511600	Weak transcription	Fetal Intestine Small	intestine
7	chr21:46496400-46501600	Weak transcription	Small Intestine	intestine
8	chr21:46496400-46509000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr21:46496400-46509000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr21:46496400-46511400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr21:46496400-46511400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr21:46496400-46513000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr21:46496600-46501600	Weak transcription	Brain Angular Gyrus	brain
14	chr21:46496600-46511600	Weak transcription	Brain Hippocampus Middle	brain
15	chr21:46496600-46512000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr21:46497000-46502000	Genic enhancers	HSMM	muscle
18	chr21:46497000-46504600	Weak transcription	Fetal Intestine Large	intestine
19	chr21:46497600-46509200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr21:46498000-46502000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr21:46498000-46509200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr21:46498200-46501400	Enhancers	Colon Smooth Muscle	Colon
23	chr21:46498200-46501600	Enhancers	HUVEC	blood vessel
24	chr21:46498200-46502000	Enhancers	Fetal Thymus	thymus
25	chr21:46498200-46502000	Enhancers	Left Ventricle	heart
26	chr21:46498400-46501600	Enhancers	Right Atrium	heart
27	chr21:46498400-46501800	Enhancers	Spleen	Spleen
28	chr21:46498600-46502800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr21:46498600-46513000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr21:46498800-46501600	Enhancers	Right Ventricle	heart
31	chr21:46499000-46506600	Weak transcription	Fetal Brain Male	brain
32	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
33	chr21:46499200-46501600	Enhancers	Fetal Heart	heart
34	chr21:46499800-46501800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr21:46499800-46507000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr21:46499800-46509200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr21:46499800-46510400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr21:46500000-46501400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr21:46500000-46501400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr21:46500000-46501800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr21:46500000-46506800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr21:46500200-46503000	Enhancers	Rectal Smooth Muscle	rectum
44	chr21:46500400-46503000	Weak transcription	Psoas Muscle	Psoas
45	chr21:46500600-46501600	Weak transcription	Thymus	Thymus
46	chr21:46500600-46501600	Enhancers	NH-A	brain
47	chr21:46500600-46501800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr21:46500600-46501800	Enhancers	NHLF	lung
49	chr21:46500800-46501400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr21:46500800-46501400	Genic enhancers	NHEK	skin

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