Variant report

Variant	rs6076364
Chromosome Location	chr20:25556801-25556802
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	chr20:25555296..25557019-chr20:25561500..25564069,2	MCF-7	breast:
2	chr20:25552816..25556954-chr20:25564456..25567707,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13040726	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983974	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2387976	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34485039	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374701	0.89[ASN][1000 genomes]
rs3752273	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376742	0.89[ASN][1000 genomes]
rs390123	0.89[ASN][1000 genomes]
rs400357	0.89[ASN][1000 genomes]
rs404775	0.89[ASN][1000 genomes]
rs405822	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs409853	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs443009	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4815429	0.89[ASN][1000 genomes]
rs4815431	0.89[ASN][1000 genomes]
rs4815437	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037158	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6050679	0.89[ASN][1000 genomes]
rs6076343	0.89[ASN][1000 genomes]
rs6076358	0.89[ASN][1000 genomes]
rs6076366	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076369	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083845	0.89[ASN][1000 genomes]
rs6083851	0.89[ASN][1000 genomes]
rs6083860	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6083891	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107060	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115188	0.89[ASN][1000 genomes]
rs6115210	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6138593	0.89[ASN][1000 genomes]
rs869358	0.89[ASN][1000 genomes]
rs958075	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];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	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	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
15	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv912833	chr20:25539486-25595175	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6076364	ABHD12	cis	Cerebellum	GTEx
rs6076364	ABHD12	cis	Brain Pons	GTEx
rs6076364	NINL	cis	Thyroid	GTEx
rs6076364	ENTPD6	cis	cerebellum	SCAN
rs6076364	ABHD12	cis	multi-tissue	Pritchard
rs6076364	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6076364	ABHD12	cis	Temporal Cortex	GTEx
rs6076364	ABHD12	cis	Frontal Cortex	GTEx
rs6076364	ABHD12	cis	cerebellum	SCAN
rs6076364	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6076364	NINL	cis	cerebellum	SCAN
rs6076364	ABHD12	cis	lymphoblastoid	seeQTL
rs6076364	GINS1	cis	parietal	SCAN
rs6076364	NINL	cis	parietal	SCAN
rs6076364	PYGB	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
2	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr20:25531200-25559600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr20:25532600-25559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:25532600-25565000	Weak transcription	HSMMtube	muscle
6	chr20:25534800-25557600	Weak transcription	Pancreas	Pancrea
7	chr20:25534800-25561400	Weak transcription	Right Atrium	heart
8	chr20:25535000-25560000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:25535000-25561400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr20:25535800-25565000	Weak transcription	Fetal Kidney	kidney
11	chr20:25544600-25565000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr20:25544800-25559600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr20:25546000-25559800	Weak transcription	Fetal Muscle Leg	muscle
14	chr20:25546400-25559800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr20:25546400-25565000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr20:25546600-25559600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr20:25546600-25559800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr20:25547000-25557600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr20:25547000-25559600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr20:25547000-25559800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr20:25548600-25557400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr20:25548800-25565200	Weak transcription	Esophagus	oesophagus
23	chr20:25549000-25557600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:25549000-25560000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:25550600-25560000	Weak transcription	HSMM	muscle
26	chr20:25550600-25561200	Weak transcription	Gastric	stomach
27	chr20:25552000-25565000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr20:25552200-25557200	Weak transcription	Brain Germinal Matrix	brain
29	chr20:25552200-25557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr20:25552200-25564800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr20:25552800-25557200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr20:25552800-25559600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr20:25553000-25559800	Weak transcription	Fetal Intestine Large	intestine
34	chr20:25554800-25557400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr20:25554800-25559600	Weak transcription	Fetal Lung	lung
36	chr20:25555000-25559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr20:25555000-25559600	Weak transcription	NH-A	brain
38	chr20:25555200-25557600	Weak transcription	Fetal Intestine Small	intestine
39	chr20:25555200-25561200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr20:25555200-25564800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr20:25555200-25565000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr20:25555200-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr20:25555400-25557600	Weak transcription	Ovary	ovary
44	chr20:25555400-25557800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr20:25555400-25559800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr20:25555400-25561200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr20:25555400-25565000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr20:25555400-25565000	Weak transcription	Brain Anterior Caudate	brain
49	chr20:25555400-25565000	Weak transcription	NHLF	lung
50	chr20:25555600-25557800	Strong transcription	A549	lung

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