Variant report

Variant	rs6505747
Chromosome Location	chr18:12305038-12305039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr18:12304957-12305177	HepG2	liver:	n/a	n/a
2	CHD2	chr18:12304794-12305349	K562	blood:	n/a	n/a
3	RCOR1	chr18:12304849-12305219	K562	blood:	n/a	n/a
4	POLR2A	chr18:12304971-12316847	IMR90	lung:	n/a	n/a
5	FOXA1	chr18:12304891-12305172	ECC-1	luminal epithelium:	n/a	n/a
6	FOS	chr18:12304950-12305180	MCF10A-Er-Src	breast:	n/a	n/a
7	FOXA1	chr18:12304905-12305195	HepG2	liver:	n/a	n/a
8	MYC	chr18:12304941-12305256	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr18:12304910-12305086	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr18:12305021-12305208	MCF10A-Er-Src	breast:	n/a	n/a
11	FOXA1	chr18:12304971-12305163	T-47D	breast:	n/a	n/a
12	FOXA2	chr18:12304858-12305207	A549	lung:	n/a	n/a
13	FOXA1	chr18:12304928-12305150	T-47D	breast:	n/a	n/a
14	BHLHE40	chr18:12304985-12305198	K562	blood:	n/a	n/a
15	FOS	chr18:12304930-12305180	MCF10A-Er-Src	breast:	n/a	n/a
16	RCOR1	chr18:12305004-12305239	K562	blood:	n/a	n/a
17	MYC	chr18:12304999-12305200	MCF10A-Er-Src	breast:	n/a	n/a
18	FOXA1	chr18:12304923-12305276	HepG2	liver:	n/a	n/a
19	FOS	chr18:12304978-12305105	MCF10A-Er-Src	breast:	n/a	n/a
20	FOXA2	chr18:12304822-12305373	A549	lung:	n/a	n/a
21	ZBTB7A	chr18:12304856-12305038	K562	blood:	n/a	n/a
22	FOXA1	chr18:12304856-12305236	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12285640..12287691-chr18:12304617..12306840,2	MCF-7	breast:
2	chr18:12295731..12298495-chr18:12304376..12306859,2	MCF-7	breast:
3	chr18:12303398..12305461-chr18:12307257..12308973,2	MCF-7	breast:

No data

Variant related genes	Relation type
TUBB6	TF binding region
RNU6-170P	TF binding region
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11662978	1.00[YRI][hapmap]
rs12965349	1.00[AMR][1000 genomes]
rs1785338	1.00[AMR][1000 genomes]
rs4797669	0.87[YRI][hapmap]
rs4797676	1.00[AMR][1000 genomes]
rs60328033	1.00[AMR][1000 genomes]
rs61460703	1.00[AMR][1000 genomes]
rs6505752	1.00[AMR][1000 genomes]
rs7504499	0.87[AFR][1000 genomes]
rs7505123	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7506586	0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8098341	0.87[AFR][1000 genomes]
rs8098572	1.00[AMR][1000 genomes]
rs9284396	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9960329	1.00[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active 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	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6505747	ABP1	trans	lymphoblastoid	seeQTL
rs6505747	CDK14	trans	lymphoblastoid	seeQTL
rs6505747	INPP1	trans	lymphoblastoid	seeQTL
rs6505747	FAM46A	trans	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12289200-12306400	Weak transcription	Right Atrium	heart
2	chr18:12289400-12306400	Weak transcription	NHLF	lung
3	chr18:12294400-12306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:12301600-12305200	Weak transcription	Esophagus	oesophagus
5	chr18:12301800-12306200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:12303000-12305200	Weak transcription	Fetal Heart	heart
7	chr18:12303000-12306000	Enhancers	K562	blood
8	chr18:12303200-12305200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr18:12303200-12306000	Weak transcription	Placenta	Placenta
10	chr18:12303200-12306200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr18:12304400-12305200	Bivalent Enhancer	HepG2	liver
12	chr18:12304400-12305400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:12304400-12306200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr18:12304400-12306600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr18:12304400-12306600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr18:12304400-12306800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr18:12304600-12305200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr18:12304600-12306400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr18:12304600-12307000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr18:12304600-12307000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:12304800-12305200	Enhancers	Rectal Smooth Muscle	rectum
22	chr18:12304800-12305400	Bivalent Enhancer	Fetal Thymus	thymus
23	chr18:12304800-12305600	Enhancers	Pancreas	Pancrea
24	chr18:12304800-12305600	Enhancers	NHEK	skin
25	chr18:12304800-12306200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr18:12304800-12306200	Bivalent Enhancer	Fetal Stomach	stomach
27	chr18:12305000-12305200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
28	chr18:12305000-12305200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr18:12305000-12305200	Bivalent Enhancer	Fetal Brain Female	brain
30	chr18:12305000-12305200	Bivalent Enhancer	Stomach Mucosa	stomach
31	chr18:12305000-12305400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
32	chr18:12305000-12305400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
33	chr18:12305000-12305400	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr18:12305000-12305400	Enhancers	Osteobl	bone
35	chr18:12305000-12305600	Enhancers	Colon Smooth Muscle	Colon
36	chr18:12305000-12306600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:12305000-12306600	Enhancers	HMEC	breast
38	chr18:12305000-12306800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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