Variant report

Variant	rs4974497
Chromosome Location	chr3:134072530-134072531
allele	A/G
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	chr3:134072373-134074291	A549	lung:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
2	POLR2A	chr3:134071214-134074714	HUVEC	blood vessel:	n/a	n/a
3	TEAD4	chr3:134072298-134073856	ECC-1	luminal epithelium:	n/a	n/a
4	TCF7L2	chr3:134072028-134072561	PANC-1	pancreas:	n/a	chr3:134072205-134072219 chr3:134072206-134072216
5	POLR2A	chr3:134071448-134074783	HUVEC	blood vessel:	n/a	n/a
6	BCL3	chr3:134072198-134073949	A549	lung:	n/a	n/a
7	MAX	chr3:134071949-134074597	A549	lung:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
8	POLR2A	chr3:134071878-134074839	HUVEC	blood vessel:	n/a	n/a
9	NFIC	chr3:134072510-134073339	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr3:134072044-134074473	ProgFib	skin:	n/a	n/a
11	POLR2A	chr3:134071621-134074470	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr3:134071059-134074572	ECC-1	luminal epithelium:	n/a	n/a
13	SP1	chr3:134072230-134073061	A549	lung:	n/a	chr3:134073011-134073024 chr3:134072812-134072826 chr3:134072911-134072925
14	BCL3	chr3:134072238-134073667	A549	lung:	n/a	n/a
15	POLR2A	chr3:134072477-134074140	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:134071177-134074761	H1-hESC	embryonic stem cell:	n/a	n/a
17	ESR1	chr3:134072155-134072545	ECC-1	luminal epithelium:	n/a	n/a
18	JUND	chr3:134072124-134073646	SK-N-SH	brain:	n/a	n/a
19	TCF12	chr3:134071925-134074047	ECC-1	luminal epithelium:	n/a	chr3:134072159-134072169
20	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
21	MAX	chr3:134072444-134073800	MCF-7	breast:	n/a	chr3:134073303-134073313 chr3:134073289-134073299 chr3:134073568-134073577 chr3:134073263-134073273 chr3:134073317-134073327 chr3:134073367-134073376
22	RAD21	chr3:134072529-134072699	A549	lung:	n/a	n/a
23	POLR2A	chr3:134071949-134074646	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
25	TCF12	chr3:134072350-134073678	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr3:134071051-134074609	ECC-1	luminal epithelium:	n/a	n/a
27	RAD21	chr3:134070902-134074481	IMR90	lung:	n/a	chr3:134071273-134071282 chr3:134073072-134073086 chr3:134071271-134071281 chr3:134071467-134071480 chr3:134073738-134073752 chr3:134071329-134071338
28	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
29	POLR2A	chr3:134071863-134074701	U87	brain:	n/a	n/a
30	POLR2A	chr3:134071236-134074903	HUVEC	blood vessel:	n/a	n/a
31	JUND	chr3:134072433-134074114	T-47D	breast:	n/a	n/a
32	POLR2A	chr3:134071113-134074862	PANC-1	pancreas:	n/a	n/a
33	TCF12	chr3:134072334-134073582	A549	lung:	n/a	n/a
34	POLR2A	chr3:134071260-134074834	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr3:134071435-134074901	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr3:134069255-134074808	A549	lung:	n/a	n/a
37	POLR2A	chr3:134072288-134074859	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr3:134072447-134072768	U87	brain:	n/a	n/a
39	SP1	chr3:134072480-134073026	A549	lung:	n/a	chr3:134073011-134073024 chr3:134072812-134072826 chr3:134072911-134072925
40	POLR2A	chr3:134071904-134074273	U87	brain:	n/a	n/a
41	POLR2A	chr3:134072061-134074617	MCF10A-Er-Src	breast:	n/a	n/a
42	JUND	chr3:134072449-134074164	A549	lung:	n/a	n/a
43	POLR2A	chr3:134072376-134074624	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a
45	EP300	chr3:134071953-134074168	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr3:134072019-134072560	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:134071025..134073147-chr3:134182309..134183857,2	MCF-7	breast:
2	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
3	chr3:134052518..134054585-chr3:134071720..134074558,2	K562	blood:
4	chr3:134071281..134073530-chr3:134186337..134189108,2	MCF-7	breast:
5	chr3:134066447..134072766-chr3:134202428..134206376,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260633	TF binding region
RPL39P5	TF binding region
ENSG00000240006	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1111516	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708815	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11719057	0.90[ASN][1000 genomes]
rs13075185	0.90[ASN][1000 genomes]
rs1353776	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1353778	0.82[AMR][1000 genomes]
rs1466827	0.86[ASN][1000 genomes]
rs1498731	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603824	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133307	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400278	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400279	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400280	0.93[ASN][1000 genomes]
rs34341902	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951257	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773820	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3821705	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.95[ASN][1000 genomes]
rs4974485	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974487	0.84[ASN][1000 genomes]
rs4974489	0.95[ASN][1000 genomes]
rs4974491	0.95[ASN][1000 genomes]
rs4974494	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974495	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974496	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974498	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439477	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439478	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.95[ASN][1000 genomes]
rs7613066	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817900	0.95[ASN][1000 genomes]
rs9853621	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4974497	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs4974497	RP11-375I20.6	cis	Thyroid	GTEx
rs4974497	RP11-375I20.6	cis	Artery Tibial	GTEx
rs4974497	RP11-375I20.6	cis	Artery Aorta	GTEx
rs4974497	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs4974497	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs4974497	RP11-375I20.6	cis	Heart Left Ventricle	GTEx
rs4974497	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4974497	RP11-375I20.6	cis	lung	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134061400-134073000	Weak transcription	Fetal Brain Male	brain
2	chr3:134066000-134072800	Enhancers	Duodenum Mucosa	Duodenum
3	chr3:134066400-134073000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:134066600-134076200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:134066800-134073000	Weak transcription	Ovary	ovary
6	chr3:134067000-134073400	Enhancers	Pancreas	Pancrea
7	chr3:134067200-134072800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134067200-134073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:134067400-134073200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:134067400-134073200	Enhancers	Esophagus	oesophagus
11	chr3:134067600-134072800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:134067600-134073200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:134067600-134076200	Strong transcription	Brain Germinal Matrix	brain
14	chr3:134067800-134073000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:134067800-134073200	Weak transcription	NH-A	brain
16	chr3:134068400-134072800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:134068400-134073200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:134068400-134074200	Genic enhancers	Fetal Intestine Small	intestine
19	chr3:134068400-134076000	Strong transcription	Fetal Stomach	stomach
20	chr3:134068800-134073200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:134069000-134074000	Strong transcription	Fetal Brain Female	brain
22	chr3:134069000-134074600	Enhancers	Psoas Muscle	Psoas
23	chr3:134069000-134076000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:134069200-134073000	Enhancers	Gastric	stomach
25	chr3:134069200-134074600	Enhancers	Stomach Mucosa	stomach
26	chr3:134069200-134090000	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr3:134069400-134072600	Enhancers	Adipose Nuclei	Adipose
28	chr3:134069400-134072800	Strong transcription	Brain Cingulate Gyrus	brain
29	chr3:134069400-134072800	Enhancers	Left Ventricle	heart
30	chr3:134069400-134073400	Enhancers	Liver	Liver
31	chr3:134069400-134089800	Genic enhancers	Fetal Muscle Leg	muscle
32	chr3:134069600-134072800	Enhancers	A549	lung
33	chr3:134069600-134073200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:134069600-134073400	Enhancers	HepG2	liver
35	chr3:134070000-134082400	Genic enhancers	Right Ventricle	heart
36	chr3:134070200-134072600	Weak transcription	Colonic Mucosa	Colon
37	chr3:134070200-134072600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:134070200-134073000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:134070400-134072600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:134070400-134072800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:134070400-134073000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:134070400-134073600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:134070400-134075000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:134070400-134075000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:134070400-134088200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:134070600-134072800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:134070600-134072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:134070600-134073000	Weak transcription	HSMM	muscle
49	chr3:134070600-134073200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:134070600-134073200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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