Variant report

Variant	rs6115092
Chromosome Location	chr20:25207375-25207376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr20:25207308-25208662	HepG2	liver:	n/a	chr20:25207842-25207853 chr20:25207843-25207852 chr20:25207841-25207854 chr20:25207842-25207853 chr20:25207842-25207852 chr20:25207843-25207852 chr20:25207842-25207853 chr20:25207843-25207852 chr20:25207842-25207852
2	POLR2A	chr20:25207349-25208233	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr20:25207295-25208607	HepG2	liver:	n/a	n/a
4	POLR2A	chr20:25206151-25207935	A549	lung:	n/a	n/a
5	TCF12	chr20:25207307-25208364	ECC-1	luminal epithelium:	n/a	chr20:25207419-25207428
6	E2F6	chr20:25207307-25208431	A549	lung:	n/a	chr20:25207935-25207942 chr20:25208090-25208107
7	POLR2A	chr20:25206820-25208593	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25176141..25177768-chr20:25206257..25208862,2	MCF-7	breast:
2	chr20:25204544..25206460-chr20:25206464..25208599,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268302	TF binding region
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs56129418	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6050456	0.92[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs6107016	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6107023	0.92[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs6115097	0.83[EUR][1000 genomes]
rs6115115	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6115142	0.81[EUR][1000 genomes]
rs6115145	0.81[EUR][1000 genomes]
rs6115177	0.92[CEU][hapmap]
rs6115178	0.92[CEU][hapmap];1.00[TSI][hapmap]
rs73101732	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8119343	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS 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	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6115092	C20orf22	cis	multi-tissue	Pritchard
rs6115092	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6115092	HDHD4	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr20:25190600-25208400	Strong transcription	Thymus	Thymus
4	chr20:25193400-25210800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:25196800-25210400	Weak transcription	GM12878-XiMat	blood
6	chr20:25197200-25208000	Weak transcription	Primary B cells from cord blood	blood
7	chr20:25197400-25207400	Weak transcription	Fetal Brain Male	brain
8	chr20:25197400-25207400	Weak transcription	NHDF-Ad	bronchial
9	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
10	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
11	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr20:25199200-25207400	Weak transcription	Psoas Muscle	Psoas
13	chr20:25199200-25208600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr20:25199200-25210600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr20:25199200-25212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr20:25199400-25210600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr20:25200200-25207400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr20:25201200-25207400	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr20:25201600-25208200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:25202200-25207400	Weak transcription	Colon Smooth Muscle	Colon
21	chr20:25202200-25209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr20:25202800-25207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr20:25203200-25207600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr20:25204000-25207600	Strong transcription	Spleen	Spleen
25	chr20:25204000-25208200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr20:25204200-25207600	Strong transcription	Brain Cingulate Gyrus	brain
27	chr20:25204200-25208400	Strong transcription	Primary T cells from cord blood	blood
28	chr20:25204200-25208600	Strong transcription	Fetal Intestine Large	intestine
29	chr20:25204200-25213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr20:25204400-25207400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr20:25204400-25207400	Weak transcription	HSMMtube	muscle
33	chr20:25204400-25207600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr20:25204400-25207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr20:25204400-25207800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr20:25204400-25207800	Strong transcription	Dnd41	blood
37	chr20:25204400-25208000	Genic enhancers	A549	lung
38	chr20:25204400-25209200	Strong transcription	Fetal Intestine Small	intestine
39	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr20:25204600-25208000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr20:25204800-25207400	Strong transcription	Fetal Thymus	thymus
42	chr20:25204800-25207400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr20:25204800-25207600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:25204800-25207600	Weak transcription	HSMM	muscle
45	chr20:25204800-25207800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr20:25204800-25210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr20:25204800-25213600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr20:25205000-25207400	Weak transcription	K562	blood
49	chr20:25205000-25207400	Weak transcription	Osteobl	bone
50	chr20:25205000-25207600	Weak transcription	HUVEC	blood vessel

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