Variant report

Variant	rs73228752
Chromosome Location	chr3:142315446-142315447
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	SIN3AK20	chr3:142314730-142315621	PANC-1	pancreas:	n/a	n/a
2	SP1	chr3:142314306-142315771	A549	lung:	n/a	chr3:142314509-142314516 chr3:142315358-142315367
3	NRF1	chr3:142314951-142315680	Hela-S3	cervix:	n/a	chr3:142315238-142315252 chr3:142315258-142315267 chr3:142315255-142315266 chr3:142315224-142315235 chr3:142315224-142315235 chr3:142315255-142315269 chr3:142315224-142315238 chr3:142315237-142315248 chr3:142315428-142315437
4	IRF1	chr3:142314904-142315632	K562	blood:	n/a	chr3:142315401-142315418 chr3:142315145-142315165
5	TBP	chr3:142314544-142315694	K562	blood:	n/a	n/a
6	IRF1	chr3:142314644-142315483	K562	blood:	n/a	chr3:142315401-142315418 chr3:142315145-142315165 chr3:142314734-142314748
7	MAX	chr3:142314790-142315515	GM12878	blood:	n/a	n/a
8	MAX	chr3:142314260-142315902	A549	lung:	n/a	chr3:142314484-142314503 chr3:142314490-142314497 chr3:142314488-142314499 chr3:142314489-142314498
9	POLR2A	chr3:142314766-142315606	Hela-S3	cervix:	n/a	n/a
10	FOSL2	chr3:142314333-142315550	A549	lung:	n/a	n/a
11	CTCF	chr3:142315083-142315517	GM12878	blood:	n/a	chr3:142315288-142315296 chr3:142315287-142315295
12	E2F4	chr3:142314987-142315531	K562	blood:	n/a	chr3:142315258-142315267 chr3:142315424-142315433
13	POLR2A	chr3:142314693-142315661	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr3:142314770-142315556	ProgFib	skin:	n/a	n/a
15	SRF	chr3:142314726-142315613	ECC-1	luminal epithelium:	n/a	n/a
16	ELF1	chr3:142314925-142315537	GM12878	blood:	n/a	chr3:142315339-142315351
17	POLR2A	chr3:142314652-142315473	MCF10A-Er-Src	breast:	n/a	n/a
18	TEAD4	chr3:142314272-142315694	HepG2	liver:	n/a	n/a
19	FOSL2	chr3:142314877-142315470	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:142314939-142315492	Hela-S3	cervix:	n/a	n/a
21	TAF1	chr3:142314773-142315495	K562	blood:	n/a	n/a
22	EP300	chr3:142314307-142315790	ECC-1	luminal epithelium:	n/a	chr3:142315258-142315267
23	POLR2A	chr3:142314958-142315461	H1-neurons	neurons:	n/a	n/a
24	POLR2A	chr3:142314811-142315502	HepG2	liver:	n/a	n/a
25	MAZ	chr3:142314724-142315498	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr3:142314881-142315455	K562	blood:	n/a	n/a
27	FOXA1	chr3:142314891-142315858	HepG2	liver:	n/a	chr3:142315563-142315578
28	MAX	chr3:142314890-142315729	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:142314801-142315473	HepG2	liver:	n/a	n/a
30	ZKSCAN1	chr3:142314587-142315511	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr3:142314712-142315524	GM19099	blood:	n/a	n/a
32	MAX	chr3:142314256-142315811	ECC-1	luminal epithelium:	n/a	chr3:142314484-142314503 chr3:142314490-142314497 chr3:142314488-142314499 chr3:142314489-142314498
33	CTCF	chr3:142315300-142315450	HCPEpiC	choroid plexus:	n/a	n/a
34	HDAC2	chr3:142314737-142315723	MCF-7	breast:	n/a	n/a
35	MAX	chr3:142314743-142315677	K562	blood:	n/a	n/a
36	FOXM1	chr3:142314875-142315492	GM12878	blood:	n/a	n/a
37	YY1	chr3:142314896-142315478	A549	lung:	n/a	n/a
38	POLR2A	chr3:142314886-142315728	NB4	blood:	n/a	n/a
39	POLR2A	chr3:142314644-142315485	K562	blood:	n/a	n/a
40	MYC	chr3:142314471-142316041	K562	blood:	n/a	chr3:142314484-142314503 chr3:142314490-142314497 chr3:142314488-142314499 chr3:142314489-142314498
41	ZNF143	chr3:142315001-142315512	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:142314912-142315499	GM12878	blood:	n/a	n/a
43	MAX	chr3:142314280-142315820	HepG2	liver:	n/a	chr3:142314484-142314503 chr3:142314490-142314497 chr3:142314488-142314499 chr3:142314489-142314498
44	POLR2A	chr3:142314748-142315509	H1-hESC	embryonic stem cell:	n/a	n/a
45	MYC	chr3:142314996-142315585	MCF-7	breast:	n/a	n/a
46	E2F6	chr3:142314805-142315758	H1-hESC	embryonic stem cell:	n/a	chr3:142315258-142315267 chr3:142315152-142315163 chr3:142315424-142315433
47	POLR2A	chr3:142314687-142315559	HL-60	blood:	n/a	n/a
48	MAZ	chr3:142314705-142315605	K562	blood:	n/a	n/a
49	RUNX3	chr3:142314756-142315568	GM12878	blood:	n/a	n/a
50	BRCA1	chr3:142314590-142315794	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142297466..142299799-chr3:142313558..142315620,3	K562	blood:
2	chr3:142313766..142316499-chr3:142498136..142500635,2	K562	blood:
3	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
4	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:
5	chr19:4400062..4400737-chr3:142314856..142315795,2	HCT-116	colon:
6	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
7	chr3:133292322..133293201-chr3:142314859..142315610,2	HCT-116	colon:
8	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
9	chr3:142296149..142300233-chr3:142313670..142315817,6	K562	blood:
10	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
11	chr3:142314277..142316663-chr3:142382049..142384101,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP143	TF binding region
ENSG00000120756	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000141985	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000242390	Chromatin interaction
ENSG00000091527	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11709121	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11719960	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2272150	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73228759	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73228762	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142314200-142315600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:142314200-142317800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr3:142314400-142315600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:142314400-142315600	Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr3:142314400-142315600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:142314400-142315600	Active TSS	Colon Smooth Muscle	Colon
7	chr3:142314400-142315800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:142314400-142315800	Active TSS	Aorta	Aorta
9	chr3:142314400-142315800	Active TSS	Pancreas	Pancrea
10	chr3:142314400-142315800	Active TSS	Right Atrium	heart
11	chr3:142314400-142316000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:142314400-142316000	Active TSS	Brain Cingulate Gyrus	brain
13	chr3:142314400-142316000	Active TSS	Brain Hippocampus Middle	brain
14	chr3:142314400-142316000	Active TSS	Fetal Thymus	thymus
15	chr3:142314400-142316200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:142314400-142316200	Active TSS	A549	lung
17	chr3:142314400-142316600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr3:142314400-142316800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr3:142314400-142317200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr3:142314400-142317400	Active TSS	Colonic Mucosa	Colon
21	chr3:142314400-142317400	Active TSS	Fetal Kidney	kidney
22	chr3:142314400-142317600	Active TSS	Rectal Smooth Muscle	rectum
23	chr3:142314400-142317800	Active TSS	Duodenum Mucosa	Duodenum
24	chr3:142314600-142315600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr3:142314600-142315600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:142314600-142315600	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:142314600-142315600	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:142314600-142315600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr3:142314600-142315600	Active TSS	Primary T cells from cord blood	blood
30	chr3:142314600-142315600	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr3:142314600-142315600	Active TSS	Brain Anterior Caudate	brain
32	chr3:142314600-142315600	Active TSS	Fetal Brain Female	brain
33	chr3:142314600-142315800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:142314600-142315800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr3:142314600-142315800	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr3:142314600-142315800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:142314600-142315800	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr3:142314600-142315800	Active TSS	Esophagus	oesophagus
39	chr3:142314600-142315800	Active TSS	Left Ventricle	heart
40	chr3:142314600-142315800	Active TSS	Ovary	ovary
41	chr3:142314600-142315800	Active TSS	Psoas Muscle	Psoas
42	chr3:142314600-142315800	Active TSS	Right Ventricle	heart
43	chr3:142314600-142316000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:142314600-142316000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:142314600-142316000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:142314600-142316000	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr3:142314600-142316000	Active TSS	Brain Substantia Nigra	brain
48	chr3:142314600-142316000	Active TSS	Thymus	Thymus
49	chr3:142314600-142316000	Active TSS	NHEK	skin
50	chr3:142314600-142316200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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