Variant report

Variant	rs6076358
Chromosome Location	chr20:25519403-25519404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25512408..25515336-chr20:25515482..25519858,3	MCF-7	breast:
2	chr20:25476419..25480130-chr20:25519164..25522649,4	MCF-7	breast:
3	chr20:25518724..25523016-chr20:25601749..25604904,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13040726	0.89[ASN][1000 genomes]
rs1983974	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34485039	0.89[ASN][1000 genomes]
rs35735333	0.80[EUR][1000 genomes]
rs374701	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752273	0.89[ASN][1000 genomes]
rs376742	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390123	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs400357	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404775	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405822	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409853	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422148	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4423675	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs443009	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815413	0.82[EUR][1000 genomes]
rs4815429	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815431	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815437	0.89[ASN][1000 genomes]
rs6037158	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050679	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076343	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076364	0.89[ASN][1000 genomes]
rs6076366	0.89[ASN][1000 genomes]
rs6076369	0.89[ASN][1000 genomes]
rs6083824	0.82[EUR][1000 genomes]
rs6083845	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083851	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083860	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083891	0.89[ASN][1000 genomes]
rs6107060	0.89[ASN][1000 genomes]
rs6115188	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115210	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132845	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6138593	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869358	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958075	0.89[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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6076358	PYGB	cis	Whole Blood	GTEx
rs6076358	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6076358	NINL	cis	Thyroid	GTEx
rs6076358	ABHD12	cis	multi-tissue	Pritchard
rs6076358	PYGB	cis	multi-tissue	Pritchard
rs6076358	ABHD12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 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	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
3	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:25507600-25519600	Weak transcription	Fetal Intestine Large	intestine
5	chr20:25511200-25520200	Weak transcription	Fetal Brain Male	brain
6	chr20:25513800-25520400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr20:25513800-25521200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr20:25514200-25521000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr20:25514400-25520000	Weak transcription	NHLF	lung
10	chr20:25514400-25520800	Weak transcription	Fetal Kidney	kidney
11	chr20:25514400-25522400	Weak transcription	NH-A	brain
12	chr20:25514800-25520000	Weak transcription	Osteobl	bone
13	chr20:25514800-25520400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr20:25515000-25519600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr20:25515000-25520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:25515000-25520200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr20:25515400-25519600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr20:25515400-25520600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr20:25515600-25519600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr20:25515600-25519800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr20:25515600-25520200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr20:25515800-25519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr20:25516000-25519800	Weak transcription	Fetal Thymus	thymus
24	chr20:25516000-25520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr20:25516200-25519800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr20:25516800-25520000	Weak transcription	NHDF-Ad	bronchial
27	chr20:25517000-25519600	Weak transcription	Brain Angular Gyrus	brain
28	chr20:25517000-25519600	Weak transcription	Fetal Lung	lung
29	chr20:25517000-25519800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:25517000-25519800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:25517000-25520000	Weak transcription	Aorta	Aorta
32	chr20:25517200-25519600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr20:25517600-25519600	Strong transcription	Fetal Stomach	stomach
34	chr20:25517600-25520000	Strong transcription	Dnd41	blood
35	chr20:25517800-25519800	Strong transcription	Fetal Brain Female	brain
36	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr20:25518200-25519600	Strong transcription	Brain Germinal Matrix	brain
38	chr20:25518200-25520800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr20:25518600-25519600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr20:25518600-25520200	Enhancers	Right Ventricle	heart
41	chr20:25518800-25519600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr20:25518800-25519800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:25518800-25521000	Weak transcription	A549	lung
44	chr20:25518800-25524400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr20:25518800-25530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr20:25519000-25519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr20:25519000-25519800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr20:25519000-25519800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr20:25519000-25521800	Weak transcription	Thymus	Thymus
50	chr20:25519000-25522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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