Variant report

Variant	rs422148
Chromosome Location	chr20:25512604-25512605
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25512408..25515336-chr20:25515482..25519858,3	MCF-7	breast:
2	chr20:25499922..25502486-chr20:25510143..25513350,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1983974	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35735333	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs374701	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs376742	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs390123	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs400357	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs404775	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs405822	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs409853	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4423675	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs443009	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815413	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4815429	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4815431	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6037158	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050679	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6076343	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6076358	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083824	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6083845	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083851	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083860	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6115188	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6115210	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132845	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138593	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs869358	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
17	nsv979406	chr20:25509600-25513942	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs422148	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs422148	PYGB	cis	multi-tissue	Pritchard
rs422148	NINL	cis	Thyroid	GTEx
rs422148	PYGB	cis	Whole Blood	GTEx
rs422148	ABHD12	cis	multi-tissue	Pritchard
rs422148	GINS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
2	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
3	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
5	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr20:25498200-25512800	Weak transcription	Adipose Nuclei	Adipose
7	chr20:25498200-25513000	Weak transcription	Fetal Thymus	thymus
8	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
9	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr20:25498200-25519400	Weak transcription	Gastric	stomach
11	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr20:25498600-25512800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
15	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr20:25504800-25512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr20:25505000-25512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:25505200-25512800	Weak transcription	Esophagus	oesophagus
19	chr20:25505200-25513800	Weak transcription	Fetal Kidney	kidney
20	chr20:25505400-25513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr20:25505400-25514600	Weak transcription	Lung	lung
22	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:25507000-25512800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr20:25507200-25513400	Weak transcription	Fetal Lung	lung
25	chr20:25507400-25512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:25507400-25518400	Weak transcription	A549	lung
27	chr20:25507600-25512800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr20:25507600-25512800	Weak transcription	HMEC	breast
29	chr20:25507600-25512800	Weak transcription	Osteobl	bone
30	chr20:25507600-25513000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr20:25507600-25513400	Weak transcription	Liver	Liver
32	chr20:25507600-25513600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:25507600-25513600	Weak transcription	NHLF	lung
34	chr20:25507600-25518000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr20:25507600-25519600	Weak transcription	Fetal Intestine Large	intestine
36	chr20:25507800-25512800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:25507800-25513000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr20:25507800-25513000	Weak transcription	NH-A	brain
39	chr20:25507800-25513200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:25507800-25516800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:25509000-25513200	Weak transcription	HepG2	liver
42	chr20:25511200-25517600	Weak transcription	Fetal Brain Female	brain
43	chr20:25511200-25520200	Weak transcription	Fetal Brain Male	brain
44	chr20:25511600-25513400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr20:25511800-25512800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr20:25512000-25516000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr20:25512200-25512800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr20:25512200-25512800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr20:25512200-25513200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr20:25512200-25513200	ZNF genes & repeats	Fetal Stomach	stomach

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