Variant report

Variant	rs2500445
Chromosome Location	chr20:25337496-25337497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25307435..25309771-chr20:25337246..25338964,2	MCF-7	breast:
2	chr20:25328148..25330867-chr20:25336121..25338656,2	MCF-7	breast:
3	chr20:25334830..25338247-chr20:25338696..25341660,3	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs2039400	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2210053	1.00[ASN][1000 genomes]
rs2258671	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2258672	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2474768	1.00[AMR][1000 genomes]
rs2474770	1.00[AMR][1000 genomes]
rs2474772	1.00[AMR][1000 genomes]
rs2474775	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2474776	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482907	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482916	1.00[AMR][1000 genomes]
rs2482917	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482920	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482922	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482925	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482929	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482939	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482942	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2482945	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500394	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500396	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500402	1.00[AMR][1000 genomes]
rs2500407	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500409	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500411	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2500412	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500414	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500416	1.00[ASN][1000 genomes]
rs2500419	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500420	1.00[AMR][1000 genomes]
rs2500428	1.00[ASN][1000 genomes]
rs2500429	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500431	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500434	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500435	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2500437	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500440	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500447	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2983490	1.00[AMR][1000 genomes]
rs2990514	1.00[ASN][1000 genomes]
rs2990515	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002699	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3002703	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs364722	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs366060	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368636	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs368748	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs371447	1.00[ASN][1000 genomes]
rs378534	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs379538	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380021	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs384336	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs388007	1.00[ASN][1000 genomes]
rs394798	1.00[ASN][1000 genomes]
rs400916	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs409873	1.00[ASN][1000 genomes]
rs409888	1.00[ASN][1000 genomes]
rs417446	1.00[ASN][1000 genomes]
rs417662	1.00[ASN][1000 genomes]
rs423248	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs426143	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs428801	1.00[ASN][1000 genomes]
rs429120	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs432403	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs439642	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs442728	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448212	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs448866	1.00[AMR][1000 genomes]
rs518336	1.00[AMR][1000 genomes]
rs56165312	1.00[ASN][1000 genomes]
rs59222176	1.00[ASN][1000 genomes]
rs6037089	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6037112	1.00[ASN][1000 genomes]
rs6037113	1.00[ASN][1000 genomes]
rs6037119	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60483717	1.00[ASN][1000 genomes]
rs6050591	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050613	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050618	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050627	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050628	1.00[ASN][1000 genomes]
rs6115206	1.00[ASN][1000 genomes]
rs73904036	1.00[AMR][1000 genomes]
rs73904038	1.00[AMR][1000 genomes]
rs73904039	1.00[AMR][1000 genomes]
rs73904476	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73907308	1.00[ASN][1000 genomes]
rs73907312	1.00[ASN][1000 genomes]
rs73907315	1.00[ASN][1000 genomes]
rs913790	1.00[ASN][1000 genomes]
rs913791	1.00[ASN][1000 genomes]
rs913793	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	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
3	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	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
9	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
11	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
12	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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
16	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
2	chr20:25319200-25348400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood
4	chr20:25333400-25338800	Enhancers	Brain Substantia Nigra	brain
5	chr20:25333600-25339200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr20:25333600-25339400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr20:25334000-25338000	Enhancers	Brain Anterior Caudate	brain
8	chr20:25334000-25338600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:25334000-25339000	Enhancers	Pancreas	Pancrea
10	chr20:25334000-25339400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:25334200-25338000	Enhancers	Left Ventricle	heart
12	chr20:25334200-25338000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr20:25334200-25339200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr20:25334200-25339400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr20:25334200-25339600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr20:25334600-25339200	Weak transcription	Esophagus	oesophagus
17	chr20:25334600-25339200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr20:25334600-25341600	Weak transcription	NHLF	lung
19	chr20:25334600-25353600	Weak transcription	Aorta	Aorta
20	chr20:25334600-25357600	Weak transcription	Fetal Muscle Leg	muscle
21	chr20:25334800-25351000	Weak transcription	Fetal Intestine Small	intestine
22	chr20:25334800-25362600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr20:25335000-25339000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr20:25335200-25339200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:25335600-25338000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr20:25335600-25341400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:25335800-25337800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr20:25335800-25341400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr20:25335800-25350200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr20:25336000-25337600	Enhancers	Primary hematopoietic stem cells	blood
31	chr20:25336000-25338800	Enhancers	GM12878-XiMat	blood
32	chr20:25336000-25339400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr20:25336000-25341400	Weak transcription	Fetal Lung	lung
34	chr20:25336200-25341400	Weak transcription	Primary B cells from cord blood	blood
35	chr20:25336400-25337800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:25336400-25338000	Enhancers	Fetal Brain Female	brain
37	chr20:25336600-25337600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:25336600-25337600	Enhancers	Right Atrium	heart
39	chr20:25336600-25337600	Enhancers	Spleen	Spleen
40	chr20:25336600-25337800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr20:25336600-25338000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr20:25336600-25338200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr20:25336600-25338200	Enhancers	Right Ventricle	heart
44	chr20:25336600-25338400	Enhancers	Fetal Heart	heart
45	chr20:25336600-25339200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr20:25336600-25339400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr20:25336600-25339400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr20:25336800-25337600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr20:25336800-25337600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr20:25336800-25337600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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