Variant report

Variant	rs12625748
Chromosome Location	chr20:25326700-25326701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25324909..25327111-chr20:25375106..25376972,2	MCF-7	breast:
2	chr20:25326249..25327757-chr20:25332487..25334812,2	MCF-7	breast:
3	chr20:25326532..25328200-chr20:25370119..25372568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11696666	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11699392	0.82[JPT][hapmap]
rs11699872	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs12480853	0.90[JPT][hapmap]
rs12480898	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12481409	0.86[EUR][1000 genomes]
rs12625157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1962310	0.99[ASN][1000 genomes]
rs2050097	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2274890	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2281212	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2281558	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2281561	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2281562	0.89[ASN][1000 genomes]
rs35084391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736720	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764694	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3787080	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6115202	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs66807280	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs68053392	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8115509	0.83[JPT][hapmap]
rs9305141	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25292000-25327400	Weak transcription	Aorta	Aorta
2	chr20:25292600-25351600	Weak transcription	NHDF-Ad	bronchial
3	chr20:25304400-25327000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr20:25305000-25327000	Weak transcription	Primary T cells from cord blood	blood
5	chr20:25305000-25331800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr20:25305400-25335000	Weak transcription	Primary B cells from cord blood	blood
7	chr20:25306200-25335800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr20:25309600-25333200	Weak transcription	NHLF	lung
9	chr20:25310200-25332000	Weak transcription	Colon Smooth Muscle	Colon
10	chr20:25310400-25334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr20:25310600-25334200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:25311400-25327000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr20:25317000-25327600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:25317600-25335600	Weak transcription	Small Intestine	intestine
15	chr20:25319200-25334200	Weak transcription	Right Ventricle	heart
16	chr20:25319200-25348400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr20:25319400-25337000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr20:25319600-25328600	Weak transcription	Fetal Stomach	stomach
19	chr20:25319600-25331400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:25319600-25334600	Weak transcription	Fetal Brain Female	brain
21	chr20:25319600-25337000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr20:25319800-25327000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr20:25319800-25334400	Weak transcription	Fetal Kidney	kidney
24	chr20:25320000-25336800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr20:25321200-25331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr20:25321200-25334200	Weak transcription	Ovary	ovary
27	chr20:25321400-25331800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr20:25322200-25334200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr20:25322400-25336600	Weak transcription	Fetal Heart	heart
30	chr20:25322600-25327000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr20:25322800-25331000	Weak transcription	Fetal Intestine Small	intestine
32	chr20:25323400-25333400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:25323600-25333000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr20:25323600-25333200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr20:25324200-25331000	Weak transcription	Pancreas	Pancrea
36	chr20:25324200-25333400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:25324200-25337200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr20:25324400-25334200	Weak transcription	Left Ventricle	heart
39	chr20:25324800-25327200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr20:25325200-25326800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr20:25325400-25331400	Weak transcription	Brain Angular Gyrus	brain
42	chr20:25325400-25334200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr20:25325400-25334200	Weak transcription	GM12878-XiMat	blood
44	chr20:25325400-25336600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr20:25325600-25327000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr20:25325600-25331400	Weak transcription	Brain Hippocampus Middle	brain
47	chr20:25325600-25333600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr20:25325600-25334200	Weak transcription	A549	lung
49	chr20:25325600-25336600	Weak transcription	Dnd41	blood
50	chr20:25326000-25326800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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