Variant report

Variant	rs885402
Chromosome Location	chr20:24898856-24898857
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24283582..24284398-chr20:24898678..24899422,2	MCF-7	breast:
2	chr20:24892772..24894924-chr20:24896880..24898878,2	MCF-7	breast:
3	chr20:24764501..24765530-chr20:24898693..24899347,4	MCF-7	breast:
4	chr20:24763298..24765600-chr20:24898179..24900035,23	MCF-7	breast:
5	chr20:24814781..24815580-chr20:24898686..24899395,4	MCF-7	breast:
6	chr20:24771465..24772208-chr20:24898686..24899202,2	MCF-7	breast:
7	chr20:24887755..24889606-chr20:24897276..24899425,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12479636	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064404	1.00[CHB][hapmap]
rs4239751	1.00[CHB][hapmap]
rs4462847	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4502500	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815358	1.00[CHB][hapmap]
rs4815359	1.00[CHB][hapmap]
rs56183883	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036967	0.80[AMR][1000 genomes]
rs6036968	0.80[AMR][1000 genomes]
rs6036972	0.80[AMR][1000 genomes]
rs6050114	0.80[AMR][1000 genomes]
rs6050115	0.80[AMR][1000 genomes]
rs6050117	0.86[AMR][1000 genomes]
rs6050119	0.86[AMR][1000 genomes]
rs6050120	0.86[AMR][1000 genomes]
rs6050121	1.00[ASN][1000 genomes]
rs6050122	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6050124	1.00[ASN][1000 genomes]
rs6050125	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050127	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083697	1.00[CHB][hapmap]
rs6083714	1.00[CHB][hapmap]
rs6106969	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6114921	0.80[AMR][1000 genomes]
rs761368	1.00[CHB][hapmap]
rs765834	1.00[CHB][hapmap]
rs914309	1.00[ASN][1000 genomes]
rs914310	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs914311	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs914313	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914315	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944503	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961218	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers 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	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv432115	chr20:24871385-24915839	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058559	chr20:24880415-24923818	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1061536	chr20:24880777-24930642	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1060158	chr20:24887819-24918081	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1066090	chr20:24887819-24923818	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1065568	chr20:24887819-24925706	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv518411	chr20:24897355-24898856	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv524921	chr20:24897355-24932028	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs885402	ACSS1	cis	cerebellum	SCAN
rs885402	C20orf3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24898000-24899600	Enhancers	Brain Hippocampus Middle	brain
2	chr20:24898400-24899800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:24898400-24900600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:24898600-24899000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:24898600-24899000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr20:24898600-24899200	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr20:24898600-24899600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr20:24898600-24899600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:24898600-24899800	Enhancers	Fetal Lung	lung
10	chr20:24898600-24899800	Bivalent Enhancer	Fetal Stomach	stomach
11	chr20:24898600-24899800	Enhancers	GM12878-XiMat	blood
12	chr20:24898600-24900000	Enhancers	Adipose Nuclei	Adipose
13	chr20:24898600-24901400	Enhancers	Placenta	Placenta
14	chr20:24898800-24899000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:24898800-24899000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr20:24898800-24899000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr20:24898800-24899000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr20:24898800-24899000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr20:24898800-24899200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr20:24898800-24899200	Enhancers	Primary B cells from peripheral blood	blood
21	chr20:24898800-24899200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr20:24898800-24899200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr20:24898800-24899200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:24898800-24899200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:24898800-24899200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr20:24898800-24899200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr20:24898800-24899200	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr20:24898800-24899200	Bivalent/Poised TSS	HepG2	liver
29	chr20:24898800-24899400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr20:24898800-24899400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr20:24898800-24899400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr20:24898800-24899400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr20:24898800-24899400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
34	chr20:24898800-24899400	Enhancers	Fetal Brain Female	brain
35	chr20:24898800-24899600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr20:24898800-24899600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr20:24898800-24899600	Enhancers	Brain Angular Gyrus	brain
38	chr20:24898800-24899600	Enhancers	Fetal Brain Male	brain
39	chr20:24898800-24899600	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr20:24898800-24899600	Enhancers	Thymus	Thymus
41	chr20:24898800-24899600	Enhancers	HSMM	muscle
42	chr20:24898800-24899600	Bivalent Enhancer	Osteobl	bone
43	chr20:24898800-24899800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:24898800-24899800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr20:24898800-24899800	Active TSS	Colonic Mucosa	Colon
46	chr20:24898800-24899800	Enhancers	Colon Smooth Muscle	Colon
47	chr20:24898800-24899800	Enhancers	Esophagus	oesophagus
48	chr20:24898800-24899800	Enhancers	Fetal Thymus	thymus
49	chr20:24898800-24900000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr20:24898800-24901600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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