Variant report

Variant	rs41292370
Chromosome Location	chr3:52541424-52541425
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	FOSL2	chr3:52541410-52541752	A549	lung:	n/a	n/a
2	NR3C1	chr3:52541374-52541771	A549	lung:	n/a	n/a
3	FOXA2	chr3:52541292-52541696	A549	lung:	n/a	chr3:52541578-52541590
4	FOXA1	chr3:52541397-52541803	HepG2	liver:	n/a	chr3:52541578-52541590
5	MAX	chr3:52541398-52541963	HepG2	liver:	n/a	n/a
6	FOSL2	chr3:52541359-52541771	HepG2	liver:	n/a	n/a
7	FOXA1	chr3:52541355-52541686	HepG2	liver:	n/a	chr3:52541578-52541590
8	NR3C1	chr3:52541412-52541731	A549	lung:	n/a	n/a
9	FOXA1	chr3:52541381-52541694	HepG2	liver:	n/a	chr3:52541578-52541590
10	FOXA1	chr3:52541402-52541707	HepG2	liver:	n/a	chr3:52541578-52541590
11	MXI1	chr3:52541329-52541964	IMR90	lung:	n/a	n/a
12	TEAD4	chr3:52541268-52541676	HepG2	liver:	n/a	n/a
13	MAZ	chr3:52541264-52541957	IMR90	lung:	n/a	n/a
14	E2F6	chr3:52541365-52541879	A549	lung:	n/a	n/a
15	USF1	chr3:52541397-52541827	A549	lung:	n/a	chr3:52541661-52541672
16	MAX	chr3:52541393-52541922	A549	lung:	n/a	n/a
17	POLR2A	chr3:52541409-52541718	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr3:52541246-52541820	HUVEC	blood vessel:	n/a	n/a
19	FOXA2	chr3:52541300-52541776	A549	lung:	n/a	chr3:52541578-52541590

No.	Distal block	Cell Line	Cell type
1	chr3:52541025..52543370-chr3:52561947..52564840,2	K562	blood:
2	chr3:52539372..52542636-chr3:52569567..52572921,4	MCF-7	breast:
3	chr3:52539792..52541522-chr3:52570415..52572331,2	K562	blood:

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs28997577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35491443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41292362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41292366	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56326215	1.00[EUR][1000 genomes]
rs59078569	1.00[EUR][1000 genomes]
rs59410274	1.00[EUR][1000 genomes]
rs61418167	1.00[EUR][1000 genomes]
rs61729402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61729450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61734637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61734643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61734653	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61736838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61739897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52530200-52551800	Weak transcription	Esophagus	oesophagus
2	chr3:52530400-52552400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52530800-52548200	Weak transcription	Right Ventricle	heart
5	chr3:52530800-52551600	Weak transcription	Fetal Intestine Small	intestine
6	chr3:52531000-52547600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:52533400-52549200	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:52533400-52549200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:52533400-52559800	Weak transcription	Liver	Liver
11	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:52535600-52541600	Strong transcription	Lung	lung
14	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:52536800-52542000	Weak transcription	Fetal Stomach	stomach
17	chr3:52536800-52552600	Strong transcription	Adipose Nuclei	Adipose
18	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52538400-52548200	Weak transcription	Colonic Mucosa	Colon
20	chr3:52538800-52544200	Weak transcription	Pancreas	Pancrea
21	chr3:52539000-52546000	Strong transcription	Spleen	Spleen
22	chr3:52539800-52541600	Genic enhancers	HUVEC	blood vessel
23	chr3:52540000-52553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:52540400-52541600	Weak transcription	Thymus	Thymus
25	chr3:52540400-52541800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:52540400-52542000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:52540400-52542200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:52540400-52542200	Enhancers	Placenta	Placenta
29	chr3:52540800-52541600	Enhancers	HepG2	liver
30	chr3:52540800-52542000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:52540800-52542000	Enhancers	HSMM	muscle
32	chr3:52540800-52542200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:52540800-52549000	Weak transcription	Gastric	stomach
34	chr3:52541000-52541800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:52541000-52542400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:52541000-52543800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:52541200-52541800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:52541200-52542000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:52541400-52541600	Enhancers	NH-A	brain
40	chr3:52541400-52541600	Enhancers	Osteobl	bone
41	chr3:52541400-52542000	Enhancers	A549	lung

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