Variant report

Variant	rs28365824
Chromosome Location	chr3:142315114-142315115
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:450)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:450 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP4	chr3:142314871-142315415	H1-hESC	embryonic stem cell:	n/a	n/a
2	SMC3	chr3:142314465-142315303	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr3:142314730-142315621	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr3:142314945-142315334	HepG2	liver:	n/a	n/a
5	JUND	chr3:142314467-142315364	H1-hESC	embryonic stem cell:	n/a	chr3:142314619-142314630
6	E2F6	chr3:142315007-142315370	K562	blood:	n/a	chr3:142315258-142315267 chr3:142315152-142315163
7	SP1	chr3:142314306-142315771	A549	lung:	n/a	chr3:142314509-142314516 chr3:142315358-142315367
8	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
9	TAF1	chr3:142315011-142315238	GM12892	blood:	n/a	n/a
10	IRF1	chr3:142314904-142315632	K562	blood:	n/a	chr3:142315401-142315418 chr3:142315145-142315165
11	POLR2A	chr3:142314895-142315266	GM12892	blood:	n/a	n/a
12	TBP	chr3:142314544-142315694	K562	blood:	n/a	n/a
13	IKZF1	chr3:142314838-142315173	GM12878	blood:	n/a	n/a
14	CTCF	chr3:142315104-142315265	Spleen_OC	spleen:	n/a	n/a
15	BACH1	chr3:142314989-142315328	K562	blood:	n/a	n/a
16	IRF1	chr3:142314644-142315483	K562	blood:	n/a	chr3:142315401-142315418 chr3:142315145-142315165 chr3:142314734-142314748
17	MAX	chr3:142314790-142315515	GM12878	blood:	n/a	n/a
18	MAX	chr3:142314260-142315902	A549	lung:	n/a	chr3:142314484-142314503 chr3:142314490-142314497 chr3:142314488-142314499 chr3:142314489-142314498
19	EP300	chr3:142314762-142315334	K562	blood:	n/a	chr3:142315258-142315267
20	POLR2A	chr3:142314710-142315394	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:142314766-142315606	Hela-S3	cervix:	n/a	n/a
22	FOSL2	chr3:142314333-142315550	A549	lung:	n/a	n/a
23	POLR2A	chr3:142314856-142315289	H1-hESC	embryonic stem cell:	n/a	n/a
24	FOSL2	chr3:142315022-142315329	A549	lung:	n/a	n/a
25	CTCF	chr3:142315083-142315517	GM12878	blood:	n/a	chr3:142315288-142315296 chr3:142315287-142315295
26	E2F4	chr3:142314987-142315531	K562	blood:	n/a	chr3:142315258-142315267 chr3:142315424-142315433
27	POLR2A	chr3:142314693-142315661	SK-N-MC	brain:	n/a	n/a
28	MAFK	chr3:142314532-142315304	HepG2	liver:	n/a	n/a
29	SP1	chr3:142314639-142315416	H1-hESC	embryonic stem cell:	n/a	chr3:142315358-142315367
30	ELF1	chr3:142314664-142315382	A549	lung:	n/a	chr3:142315339-142315351
31	POLR2A	chr3:142314770-142315556	ProgFib	skin:	n/a	n/a
32	TCF12	chr3:142314703-142315382	A549	lung:	n/a	n/a
33	SRF	chr3:142314726-142315613	ECC-1	luminal epithelium:	n/a	n/a
34	ELF1	chr3:142314925-142315537	GM12878	blood:	n/a	chr3:142315339-142315351
35	POLR2A	chr3:142314652-142315473	MCF10A-Er-Src	breast:	n/a	n/a
36	BRCA1	chr3:142314966-142315337	HepG2	liver:	n/a	n/a
37	TEAD4	chr3:142314272-142315694	HepG2	liver:	n/a	n/a
38	TBP	chr3:142314531-142315301	Hela-S3	cervix:	n/a	n/a
39	FOSL2	chr3:142314877-142315470	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:142314939-142315492	Hela-S3	cervix:	n/a	n/a
41	TAF1	chr3:142314773-142315495	K562	blood:	n/a	n/a
42	ELK1	chr3:142314843-142315341	K562	blood:	n/a	n/a
43	RFX5	chr3:142314975-142315404	K562	blood:	n/a	n/a
44	MXI1	chr3:142314846-142315273	K562	blood:	n/a	n/a
45	EP300	chr3:142314307-142315790	ECC-1	luminal epithelium:	n/a	chr3:142315258-142315267
46	ATF2	chr3:142314925-142315425	GM12878	blood:	n/a	n/a
47	TAF1	chr3:142314771-142315391	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:142314958-142315461	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr3:142314811-142315502	HepG2	liver:	n/a	n/a
50	MAZ	chr3:142314724-142315498	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142315064-142315114	SK-N-SH	brain:	n/a
2	chr3:142315064-142315114	T-47D	breast:	n/a
3	chr3:142315064-142315114	HMEC	breast:	n/a
4	chr3:142315064-142315114	MCF10A-Er-Src	breast:	n/a
5	chr3:142315064-142315114	HRPEpiC	eye:	n/a
6	chr3:142315064-142315114	HEEpiC	esophagus:	n/a
7	chr3:142315064-142315114	HUVEC	blood vessel:	n/a
8	chr3:142315064-142315114	AG09319	gingival:	n/a
9	chr3:142315064-142315114	NT2-D1	testis:	n/a
10	chr3:142315064-142315114	Hela-S3	cervix:	n/a
11	chr3:142315064-142315114	GM12878	blood:	n/a
12	chr3:142315064-142315114	HRCEpiC	kidney:	n/a
13	chr3:142315064-142315114	RPTEC	kidney:	n/a
14	chr3:142315064-142315114	K562	blood:	n/a
15	chr3:142315064-142315114	U87	brain:	n/a
16	chr3:142315064-142315114	BJ	skin:	n/a
17	chr3:142315064-142315114	HRE	kidney:	n/a
18	chr3:142315064-142315114	IMR90	lung:	fetal
19	chr3:142315064-142315114	AG04449	skin:	fetal
20	chr3:142315064-142315114	NHDF-neo	bronchial:	n/a
21	chr3:142315064-142315114	LNCaP	prostate:	n/a
22	chr3:142315064-142315114	HCPEpiC	choroid plexus:	n/a
23	chr3:142315064-142315114	SKMC	muscle:	n/a
24	chr3:142315064-142315114	PFSK-1	brain:	n/a
25	chr3:142315064-142315114	Jurkat	blood:	n/a
26	chr3:142315064-142315114	GM06990	blood:	n/a
27	chr3:142315064-142315114	SK-N-SH_RA	brain:	n/a
28	chr3:142315064-142315114	AG04450	lung:	fetal
29	chr3:142315064-142315114	HIPEpiC	eye:	n/a
30	chr3:142315064-142315114	PANC-1	pancreas:	n/a
31	chr3:142315064-142315114	GM12892	blood:	n/a
32	chr3:142315064-142315114	ProgFib	skin:	n/a
33	chr3:142315064-142315114	HCT-116	colon:	n/a
34	chr3:142315064-142315114	HL-60	blood:	n/a
35	chr3:142315064-142315114	MCF-7	breast:	n/a
36	chr3:142315064-142315114	NHBE	bronchial:	n/a
37	chr3:142315064-142315114	GM12891	blood:	n/a
38	chr3:142315064-142315114	ovcar-3	ovarian:	n/a
39	chr3:142315064-142315114	SK-N-MC	brain:	n/a
40	chr3:142315064-142315114	PrEC	prostate:	n/a
41	chr3:142315064-142315114	GM19239	blood:	n/a
42	chr3:142315064-142315114	CMK	blood:	n/a
43	chr3:142315064-142315114	HEK293	kidney:	embryo
44	chr3:142315064-142315114	HNPCEpiC	eye:	n/a
45	chr3:142315064-142315114	BE2_C	brain:	n/a
46	chr3:142315064-142315114	SAEC	small airway:	n/a
47	chr3:142315064-142315114	NB4	blood:	n/a
48	chr3:142315064-142315114	HPAEpiC	pulmonary alveolar:	n/a
49	chr3:142315064-142315114	Hepatocyte	liver:	n/a
50	chr3:142315064-142315114	Caco-2	colon:	n/a

(count:12 , 50 per page) page: 1

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	chr3:142314785..142315321-chr8:33370240..33370887,2	HCT-116	colon:
7	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
8	chr3:133292322..133293201-chr3:142314859..142315610,2	HCT-116	colon:
9	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
10	chr3:142296149..142300233-chr3:142313670..142315817,6	K562	blood:
11	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
12	chr3:142314277..142316663-chr3:142382049..142384101,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP143	TF binding region
PLS1	TF binding region
PLS1	CpG island
RNA5SP143	CpG island
ENSG00000242390	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000141985	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000091527	Chromatin interaction
ENSG00000129696	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10935464	0.88[EUR][1000 genomes]
rs11711434	0.84[ASN][1000 genomes]
rs17623058	0.83[ASN][1000 genomes]
rs2229032	0.85[EUR][1000 genomes]
rs28647471	0.81[ASN][1000 genomes]
rs28709617	0.81[ASN][1000 genomes]
rs3922731	0.88[EUR][1000 genomes]
rs4398471	0.81[ASN][1000 genomes]
rs55994893	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56161530	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs56383228	0.81[ASN][1000 genomes]
rs56397702	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60001529	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440095	0.82[ASN][1000 genomes]
rs6440096	0.81[ASN][1000 genomes]
rs6440097	0.81[ASN][1000 genomes]
rs66597875	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73228757	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73228758	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73228762	0.86[ASN][1000 genomes]
rs73228782	0.83[ASN][1000 genomes]
rs73238195	0.82[EUR][1000 genomes]
rs73238200	0.88[EUR][1000 genomes]
rs73238202	0.88[EUR][1000 genomes]
rs73240305	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73240309	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73240310	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73240314	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73240316	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73240318	0.84[EUR][1000 genomes]
rs73240323	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73240328	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7633021	0.81[ASN][1000 genomes]
rs7638338	0.81[ASN][1000 genomes]
rs7647212	0.82[ASN][1000 genomes]
rs7647497	0.82[ASN][1000 genomes]
rs9813377	0.80[ASN][1000 genomes]
rs9816128	0.81[ASN][1000 genomes]
rs9816275	0.81[ASN][1000 genomes]
rs9826463	0.81[ASN][1000 genomes]
rs9858204	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9868309	0.81[ASN][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	chr3:142314200-142315200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:142314200-142315400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
3	chr3:142314200-142315600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:142314200-142317800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr3:142314400-142315200	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr3:142314400-142315200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr3:142314400-142315400	Active TSS	Placenta Amnion	Placenta Amnion
8	chr3:142314400-142315400	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr3:142314400-142315400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr3:142314400-142315600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:142314400-142315600	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr3:142314400-142315600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:142314400-142315600	Active TSS	Colon Smooth Muscle	Colon
14	chr3:142314400-142315800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:142314400-142315800	Active TSS	Aorta	Aorta
16	chr3:142314400-142315800	Active TSS	Pancreas	Pancrea
17	chr3:142314400-142315800	Active TSS	Right Atrium	heart
18	chr3:142314400-142316000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr3:142314400-142316000	Active TSS	Brain Cingulate Gyrus	brain
20	chr3:142314400-142316000	Active TSS	Brain Hippocampus Middle	brain
21	chr3:142314400-142316000	Active TSS	Fetal Thymus	thymus
22	chr3:142314400-142316200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr3:142314400-142316200	Active TSS	A549	lung
24	chr3:142314400-142316600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:142314400-142316800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr3:142314400-142317200	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr3:142314400-142317400	Active TSS	Colonic Mucosa	Colon
28	chr3:142314400-142317400	Active TSS	Fetal Kidney	kidney
29	chr3:142314400-142317600	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:142314400-142317800	Active TSS	Duodenum Mucosa	Duodenum
31	chr3:142314600-142315200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:142314600-142315200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:142314600-142315200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:142314600-142315200	Flanking Active TSS	HSMM	muscle
35	chr3:142314600-142315200	Flanking Active TSS	HUVEC	blood vessel
36	chr3:142314600-142315400	Active TSS	Primary T cells fromperipheralblood	blood
37	chr3:142314600-142315400	Active TSS	HepG2	liver
38	chr3:142314600-142315600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr3:142314600-142315600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:142314600-142315600	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr3:142314600-142315600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr3:142314600-142315600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr3:142314600-142315600	Active TSS	Primary T cells from cord blood	blood
44	chr3:142314600-142315600	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr3:142314600-142315600	Active TSS	Brain Anterior Caudate	brain
46	chr3:142314600-142315600	Active TSS	Fetal Brain Female	brain
47	chr3:142314600-142315800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:142314600-142315800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr3:142314600-142315800	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr3:142314600-142315800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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