Variant report

Variant	rs12480853
Chromosome Location	chr20:25522959-25522960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25518724..25523016-chr20:25601749..25604904,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11698953	0.82[ASN][1000 genomes]
rs11698992	0.85[ASN][1000 genomes]
rs11699872	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11700213	0.83[ASN][1000 genomes]
rs11700297	0.82[ASN][1000 genomes]
rs11700338	0.83[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12481037	0.83[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12625157	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12625748	0.90[JPT][hapmap]
rs12625991	0.85[ASN][1000 genomes]
rs1888037	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2050097	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2072975	0.84[JPT][hapmap]
rs2235605	0.84[JPT][hapmap]
rs2235606	0.84[JPT][hapmap]
rs2235607	0.85[JPT][hapmap]
rs2263205	0.85[JPT][hapmap]
rs2281212	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2482934	0.84[JPT][hapmap]
rs2500403	0.84[JPT][hapmap]
rs35364051	0.84[JPT][hapmap]
rs3736720	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs3764694	0.89[JPT][hapmap]
rs4815438	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs55792313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56238023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57803591	0.80[ASN][1000 genomes]
rs6037190	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs6050690	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs6107050	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6115202	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6115227	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115241	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs6132842	0.84[JPT][hapmap]
rs6132861	0.84[JPT][hapmap]
rs6138569	0.84[JPT][hapmap]
rs6138595	0.83[JPT][hapmap]
rs6138598	0.84[JPT][hapmap]
rs6138599	0.84[JPT][hapmap]
rs6138601	0.84[JPT][hapmap]
rs6138616	0.84[JPT][hapmap]
rs6138639	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7260957	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs73109499	0.86[ASN][1000 genomes]
rs73597820	0.84[ASN][1000 genomes]
rs73597824	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9305141	0.83[EUR][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12480853	KIAA0980	cis	multi-tissue	Pritchard
rs12480853	ABHD12	cis	Brain Pons	GTEx
rs12480853	ABHD12	cis	Cerebellum	GTEx
rs12480853	PYGB	cis	Skin Sun Exposed Lower leg	GTEx
rs12480853	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs12480853	ABHD12	cis	Temporal Cortex	GTEx
rs12480853	ABHD12	cis	Frontal Cortex	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:25518800-25524400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr20:25518800-25530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr20:25519400-25524000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:25519600-25523000	Enhancers	Fetal Intestine Large	intestine
7	chr20:25519800-25523000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr20:25519800-25523000	Enhancers	Fetal Thymus	thymus
9	chr20:25520000-25532000	Weak transcription	Dnd41	blood
10	chr20:25520200-25529000	Weak transcription	Stomach Mucosa	stomach
11	chr20:25520400-25523200	Enhancers	Fetal Intestine Small	intestine
12	chr20:25520400-25525000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:25520600-25527400	Weak transcription	Lung	lung
14	chr20:25520600-25528800	Weak transcription	Gastric	stomach
15	chr20:25520800-25524200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr20:25520800-25524800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr20:25521000-25523000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:25521000-25530200	Weak transcription	Brain Germinal Matrix	brain
19	chr20:25521200-25523200	Enhancers	Fetal Lung	lung
20	chr20:25521200-25529200	Weak transcription	Placenta	Placenta
21	chr20:25521200-25530600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr20:25521400-25523000	Enhancers	Liver	Liver
23	chr20:25521400-25523800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr20:25521400-25523800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:25521400-25523800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:25521400-25523800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr20:25521400-25524000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr20:25521400-25524000	Weak transcription	Esophagus	oesophagus
29	chr20:25521400-25524800	Weak transcription	Fetal Kidney	kidney
30	chr20:25521400-25525000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr20:25521400-25525000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr20:25521400-25525000	Weak transcription	Brain Substantia Nigra	brain
33	chr20:25521400-25525000	Weak transcription	Fetal Heart	heart
34	chr20:25521400-25525000	Weak transcription	Fetal Muscle Leg	muscle
35	chr20:25521400-25525200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr20:25521400-25525200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr20:25521400-25525200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr20:25521400-25525200	Weak transcription	Brain Anterior Caudate	brain
39	chr20:25521400-25525200	Weak transcription	Fetal Stomach	stomach
40	chr20:25521400-25525400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:25521400-25525800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr20:25521400-25525800	Weak transcription	Brain Hippocampus Middle	brain
43	chr20:25521400-25525800	Enhancers	Osteobl	bone
44	chr20:25521400-25529200	Weak transcription	Ovary	ovary
45	chr20:25521400-25530000	Weak transcription	HSMM	muscle
46	chr20:25521400-25532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25521400-25534200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr20:25521600-25523000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr20:25521600-25523000	Enhancers	Duodenum Mucosa	Duodenum
50	chr20:25521600-25523200	Enhancers	Adipose Nuclei	Adipose

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