Variant report

Variant	rs409888
Chromosome Location	chr20:25506028-25506029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25504894..25507358-chr20:25508312..25510600,2	MCF-7	breast:
2	chr20:25503491..25506421-chr20:25552111..25554965,2	MCF-7	breast:
3	chr20:25487824..25490513-chr20:25503941..25506270,3	MCF-7	breast:

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1609701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1888038	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2039400	1.00[ASN][1000 genomes]
rs2210053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242122	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242124	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242125	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242131	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242134	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[ASN][1000 genomes]
rs2482909	1.00[ASN][1000 genomes]
rs2482916	0.81[AFR][1000 genomes]
rs2482917	1.00[ASN][1000 genomes]
rs2482925	1.00[ASN][1000 genomes]
rs2482929	1.00[ASN][1000 genomes]
rs2482939	1.00[ASN][1000 genomes]
rs2482942	1.00[ASN][1000 genomes]
rs2482945	1.00[ASN][1000 genomes]
rs2500394	1.00[ASN][1000 genomes]
rs2500396	1.00[ASN][1000 genomes]
rs2500407	1.00[ASN][1000 genomes]
rs2500409	1.00[ASN][1000 genomes]
rs2500412	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[ASN][1000 genomes]
rs2500435	1.00[ASN][1000 genomes]
rs2500437	1.00[ASN][1000 genomes]
rs2500438	1.00[ASN][1000 genomes]
rs2500440	1.00[ASN][1000 genomes]
rs2500444	1.00[ASN][1000 genomes]
rs2500445	1.00[ASN][1000 genomes]
rs2500447	1.00[ASN][1000 genomes]
rs28801689	1.00[ASN][1000 genomes]
rs2892407	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2990515	1.00[ASN][1000 genomes]
rs3002703	1.00[ASN][1000 genomes]
rs364722	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs371447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs378534	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs388007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs394798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs400916	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs409873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs417446	1.00[ASN][1000 genomes]
rs417662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs423248	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs429120	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs432403	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs439642	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs442728	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs448212	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	0.88[AFR][1000 genomes]
rs4815433	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4815434	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs518336	1.00[AFR][1000 genomes]
rs55822316	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs56751491	1.00[ASN][1000 genomes]
rs57450264	1.00[ASN][1000 genomes]
rs59122217	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59222176	1.00[ASN][1000 genomes]
rs6037089	1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6037147	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037155	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037160	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037172	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037177	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037185	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037194	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037197	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037200	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037209	1.00[ASN][1000 genomes]
rs6037213	1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	1.00[ASN][1000 genomes]
rs6050613	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6050695	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050711	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050735	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050740	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050752	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050759	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050772	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050776	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050786	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050806	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050831	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050837	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050839	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050852	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6076360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6076365	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083882	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6083887	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6115206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6132844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7263728	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73904476	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73904499	1.00[ASN][1000 genomes]
rs73907312	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]
rs73907612	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907614	1.00[ASN][1000 genomes]
rs8116049	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs913790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs913791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs913793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25491200-25506200	Weak transcription	NHLF	lung
2	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
4	chr20:25495800-25506400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:25496000-25512400	Weak transcription	Brain Angular Gyrus	brain
7	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
8	chr20:25496400-25506400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr20:25497400-25512400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr20:25497400-25512400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr20:25497600-25506400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:25497600-25507200	Weak transcription	Colonic Mucosa	Colon
14	chr20:25497600-25512600	Weak transcription	Fetal Heart	heart
15	chr20:25497800-25506400	Weak transcription	HSMMtube	muscle
16	chr20:25497800-25512200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr20:25498000-25506400	Weak transcription	Fetal Brain Male	brain
18	chr20:25498000-25506600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr20:25498000-25511000	Weak transcription	Brain Hippocampus Middle	brain
20	chr20:25498200-25506600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr20:25498200-25506600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:25498200-25507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr20:25498200-25507000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr20:25498200-25510800	Weak transcription	Brain Substantia Nigra	brain
25	chr20:25498200-25512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr20:25498200-25512200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr20:25498200-25512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr20:25498200-25512600	Weak transcription	Brain Anterior Caudate	brain
29	chr20:25498200-25512800	Weak transcription	Adipose Nuclei	Adipose
30	chr20:25498200-25513000	Weak transcription	Fetal Thymus	thymus
31	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
32	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr20:25498200-25519400	Weak transcription	Gastric	stomach
34	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr20:25498600-25512800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr20:25499000-25507000	Weak transcription	Ovary	ovary
38	chr20:25501200-25507200	Strong transcription	Fetal Lung	lung
39	chr20:25501600-25507000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr20:25501600-25507200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr20:25501800-25506200	Strong transcription	A549	lung
42	chr20:25502000-25507200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr20:25502000-25507600	Strong transcription	Dnd41	blood
44	chr20:25502400-25507200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr20:25502400-25507200	Strong transcription	Brain Germinal Matrix	brain
46	chr20:25502400-25507200	Strong transcription	Fetal Muscle Leg	muscle
47	chr20:25502600-25506200	Weak transcription	HSMM	muscle
48	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
49	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr20:25503000-25507400	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links