Variant report

Variant	rs6083877
Chromosome Location	chr20:25520939-25520940
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

Extended variants
information (count: 21 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2210052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076348	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076351	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083843	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62211494	0.93[AMR][1000 genomes];0.96[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	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6083877	ENTPD6	cis	cerebellum	SCAN
rs6083877	NINL	cis	cerebellum	SCAN
rs6083877	PYGB	cis	cerebellum	SCAN
rs6083877	NINL	cis	parietal	SCAN
rs6083877	ABHD12	cis	brain	seeQTL
rs6083877	HDHD4	cis	multi-tissue	Pritchard
rs6083877	C20orf22	cis	multi-tissue	Pritchard
rs6083877	PYGB	cis	multi-tissue	Pritchard
rs6083877	GINS1	cis	parietal	SCAN
rs6083877	ABHD12	cis	cerebellum	SCAN
rs6083877	ABHD12	trans	brain	seeQTL

Chromatin state (count:96 , 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	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25513800-25521200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr20:25514200-25521000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr20:25514400-25522400	Weak transcription	NH-A	brain
6	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr20:25518800-25521000	Weak transcription	A549	lung
8	chr20:25518800-25524400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr20:25518800-25530200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:25519000-25521800	Weak transcription	Thymus	Thymus
11	chr20:25519000-25522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:25519200-25521400	Enhancers	Pancreas	Pancrea
13	chr20:25519400-25521400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:25519400-25521400	Enhancers	Fetal Heart	heart
15	chr20:25519400-25524000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:25519600-25521200	Enhancers	Placenta	Placenta
17	chr20:25519600-25521400	Enhancers	Fetal Muscle Trunk	muscle
18	chr20:25519600-25521400	Genic enhancers	Fetal Stomach	stomach
19	chr20:25519600-25521600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr20:25519600-25522000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr20:25519600-25523000	Enhancers	Fetal Intestine Large	intestine
22	chr20:25519800-25521400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr20:25519800-25521400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr20:25519800-25521400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr20:25519800-25521600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr20:25519800-25521600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr20:25519800-25521800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr20:25519800-25523000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr20:25519800-25523000	Enhancers	Fetal Thymus	thymus
30	chr20:25520000-25521400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:25520000-25521400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr20:25520000-25521400	Active TSS	Colon Smooth Muscle	Colon
33	chr20:25520000-25521600	Active TSS	Colonic Mucosa	Colon
34	chr20:25520000-25521600	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr20:25520000-25522000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr20:25520000-25532000	Weak transcription	Dnd41	blood
37	chr20:25520200-25521000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr20:25520200-25521200	Active TSS	Right Ventricle	heart
39	chr20:25520200-25521400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr20:25520200-25521400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:25520200-25521400	Active TSS	Brain Anterior Caudate	brain
42	chr20:25520200-25521400	Active TSS	Rectal Smooth Muscle	rectum
43	chr20:25520200-25521400	Flanking Active TSS	Osteobl	bone
44	chr20:25520200-25521600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr20:25520200-25521600	Active TSS	Brain Cingulate Gyrus	brain
46	chr20:25520200-25522200	Enhancers	Fetal Brain Male	brain
47	chr20:25520200-25529000	Weak transcription	Stomach Mucosa	stomach
48	chr20:25520400-25521000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr20:25520400-25521000	Enhancers	Brain Germinal Matrix	brain
50	chr20:25520400-25521200	Enhancers	Cortex derived primary cultured neurospheres	brain

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