Variant report

Variant	rs1863868
Chromosome Location	chr3:141087623-141087624
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	JUND	chr3:141086694-141087970	HCT-116	colon:	n/a	chr3:141087277-141087288 chr3:141087860-141087872
2	MXI1	chr3:141086907-141087690	Hela-S3	cervix:	n/a	chr3:141086996-141087011
3	YY1	chr3:141087459-141087815	SK-N-SH_RA	brain:	n/a	chr3:141087702-141087710 chr3:141087697-141087716 chr3:141087699-141087721 chr3:141087698-141087710
4	POLR2A	chr3:141085195-141089788	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr3:141085146-141088115	HCT-116	colon:	n/a	n/a
6	SMARCC1	chr3:141086796-141088058	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr3:141086838-141087658	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:141087057-141089441	GM12878	blood:	n/a	n/a
9	FOSL2	chr3:141086792-141087720	HepG2	liver:	n/a	n/a
10	YY1	chr3:141087549-141087821	HepG2	liver:	n/a	chr3:141087702-141087710 chr3:141087697-141087716 chr3:141087699-141087721 chr3:141087698-141087710
11	MAX	chr3:141085836-141088223	HCT-116	colon:	n/a	n/a
12	MYC	chr3:141086871-141088512	K562	blood:	n/a	n/a
13	FOS	chr3:141087052-141087716	MCF10A-Er-Src	breast:	n/a	chr3:141087277-141087288
14	JUN	chr3:141087048-141088021	K562	blood:	n/a	chr3:141087860-141087872
15	POLR2A	chr3:141086664-141089367	GM12892	blood:	n/a	n/a
16	JUND	chr3:141086892-141087710	MCF-7	breast:	n/a	chr3:141087277-141087288
17	JUND	chr3:141084716-141088288	SK-N-SH	brain:	n/a	chr3:141084974-141084986 chr3:141087277-141087288 chr3:141087860-141087872
18	JUND	chr3:141086730-141087810	A549	lung:	n/a	chr3:141087277-141087288
19	HEY1	chr3:141086690-141087803	K562	blood:	n/a	n/a
20	JUN	chr3:141087104-141087664	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:141086831-141088553	K562	blood:	n/a	n/a
22	NR3C1	chr3:141086842-141087731	A549	lung:	n/a	chr3:141087699-141087713
23	FOSL2	chr3:141084905-141088629	A549	lung:	n/a	chr3:141088454-141088465 chr3:141088456-141088468 chr3:141084974-141084986 chr3:141088457-141088467 chr3:141087860-141087872
24	E2F6	chr3:141087426-141087801	K562	blood:	n/a	n/a
25	MAX	chr3:141084953-141088456	A549	lung:	n/a	n/a
26	JUND	chr3:141086954-141087692	Hela-S3	cervix:	n/a	chr3:141087277-141087288
27	PBX3	chr3:141086838-141087784	SK-N-SH	brain:	n/a	n/a
28	ATF2	chr3:141087012-141087695	H1-hESC	embryonic stem cell:	n/a	chr3:141087293-141087307
29	CREB1	chr3:141087043-141087700	H1-hESC	embryonic stem cell:	n/a	n/a
30	JUND	chr3:141086860-141087719	HepG2	liver:	n/a	chr3:141087277-141087288
31	JUN	chr3:141087110-141087698	HUVEC	blood vessel:	n/a	n/a
32	CREB1	chr3:141086839-141087835	K562	blood:	n/a	n/a
33	ETS1	chr3:141086856-141087715	A549	lung:	n/a	chr3:141087117-141087126 chr3:141087117-141087126 chr3:141087118-141087128 chr3:141087117-141087126
34	MAX	chr3:141087500-141087837	H1-hESC	embryonic stem cell:	n/a	n/a
35	HCFC1	chr3:141086876-141087831	K562	blood:	n/a	n/a
36	POLR2A	chr3:141084808-141089686	U87	brain:	n/a	n/a
37	POLR2A	chr3:141086778-141087916	HepG2	liver:	n/a	n/a
38	FOS	chr3:141087081-141087648	MCF10A-Er-Src	breast:	n/a	chr3:141087277-141087288
39	MAX	chr3:141087541-141087726	GM12878	blood:	n/a	n/a
40	NR3C1	chr3:141086802-141087765	A549	lung:	n/a	chr3:141087699-141087713
41	E2F6	chr3:141086888-141088203	K562	blood:	n/a	n/a
42	JUND	chr3:141087071-141087639	H1-hESC	embryonic stem cell:	n/a	chr3:141087277-141087288
43	TBP	chr3:141086762-141088065	K562	blood:	n/a	n/a
44	UBTF	chr3:141086980-141087710	K562	blood:	n/a	n/a
45	RAD21	chr3:141086894-141087839	IMR90	lung:	n/a	chr3:141087702-141087711
46	YY1	chr3:141086961-141087886	K562	blood:	n/a	chr3:141087702-141087710 chr3:141087697-141087716 chr3:141087699-141087721 chr3:141087698-141087710
47	MAZ	chr3:141086831-141088523	K562	blood:	n/a	n/a
48	MAX	chr3:141086547-141087979	HepG2	liver:	n/a	n/a
49	TEAD4	chr3:141086881-141087828	ECC-1	luminal epithelium:	n/a	n/a
50	HEY1	chr3:141086859-141087742	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141087442..141089242-chr3:141144638..141146608,2	K562	blood:
2	chr3:141026359..141029498-chr3:141087361..141089431,3	K562	blood:
3	chr3:141084115..141086523-chr3:141087109..141089663,3	MCF-7	breast:
4	chr3:141087300..141088860-chr3:141163731..141166703,2	K562	blood:
5	chr3:141087470..141089413-chr3:141153626..141156604,2	MCF-7	breast:
6	chr3:141074675..141076936-chr3:141087556..141089144,2	K562	blood:
7	chr3:141041261..141043649-chr3:141085742..141087985,3	K562	blood:
8	chr3:141041261..141045456-chr3:141085742..141089187,4	K562	blood:
9	chr3:141085384..141087888-chr3:141119776..141122327,3	MCF-7	breast:
10	chr3:141085187..141087816-chr3:141204878..141206678,4	MCF-7	breast:
11	chr3:141087440..141090679-chr3:141157733..141160398,4	K562	blood:
12	chr3:141085737..141089975-chr3:141204779..141207356,5	K562	blood:
13	chr3:141084785..141090037-chr3:141119214..141123075,16	MCF-7	breast:
14	chr3:141087607..141090329-chr3:141102679..141106167,3	K562	blood:
15	chr3:141086746..141089442-chr3:141102578..141106319,5	K562	blood:
16	chr3:141086056..141088881-chr3:141120759..141122855,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACPL2-3	chr3:141087146-141087646	NONHSAT092427
2	lnc-ACPL2-3	chr3:141087166-141087646	NONHSAT092428
3	lnc-ACPL2-3	chr3:141087332-141087646	NONHSAT092429

Variant related genes	Relation type
ENSG00000249417	TF binding region
ENSG00000155903	Chromatin interaction
ENSG00000249540	Chromatin interaction
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13098180	0.87[EUR][1000 genomes]
rs1344672	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1344674	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1346408	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1582874	0.82[CEU][hapmap]
rs1991431	0.82[CEU][hapmap]
rs2871960	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs4683603	0.95[EUR][1000 genomes]
rs6440001	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs6440003	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs6440006	0.86[CEU][hapmap]
rs6763927	0.82[CEU][hapmap]
rs6763931	0.84[CEU][hapmap]
rs6764769	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs6784404	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6808936	0.82[CEU][hapmap]
rs724016	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7613516	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7624084	0.93[CEU][hapmap]
rs7632381	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs9846396	0.81[CEU][hapmap]
rs9866391	0.90[CEU][hapmap];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141084800-141087800	Enhancers	Placenta Amnion	Placenta Amnion
2	chr3:141084800-141088400	Flanking Active TSS	A549	lung
3	chr3:141085200-141088000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:141085200-141088400	Enhancers	Small Intestine	intestine
5	chr3:141085400-141087800	Enhancers	Esophagus	oesophagus
6	chr3:141085400-141088200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:141085400-141088400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr3:141085400-141088800	Flanking Active TSS	K562	blood
9	chr3:141085800-141089200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:141085800-141094200	Weak transcription	Spleen	Spleen
11	chr3:141086000-141087800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:141086000-141093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:141086200-141088400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:141086400-141089200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:141086600-141088200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:141086600-141088200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:141086600-141089200	Flanking Active TSS	HepG2	liver
18	chr3:141086600-141089400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:141086800-141087800	Enhancers	Fetal Thymus	thymus
20	chr3:141086800-141088000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:141086800-141088000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:141086800-141088000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:141086800-141088000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:141086800-141088000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:141086800-141088000	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr3:141086800-141088000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr3:141086800-141088200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:141086800-141088200	Flanking Active TSS	NHEK	skin
29	chr3:141086800-141088400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:141086800-141088400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:141086800-141088400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr3:141086800-141088400	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr3:141086800-141088600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr3:141086800-141088600	Flanking Active TSS	Fetal Lung	lung
35	chr3:141086800-141088600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr3:141086800-141088600	Flanking Active TSS	Hela-S3	cervix
37	chr3:141086800-141088800	Flanking Active TSS	HMEC	breast
38	chr3:141086800-141089200	Flanking Active TSS	HUVEC	blood vessel
39	chr3:141086800-141089200	Flanking Active TSS	NH-A	brain
40	chr3:141087000-141087800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:141087000-141087800	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr3:141087000-141088000	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr3:141087000-141088000	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr3:141087000-141088200	Active TSS	Brain Angular Gyrus	brain
45	chr3:141087000-141088200	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr3:141087000-141089600	Enhancers	Primary B cells from peripheral blood	blood
47	chr3:141087000-141091600	Weak transcription	Gastric	stomach
48	chr3:141087000-141107800	Weak transcription	Pancreas	Pancrea
49	chr3:141087200-141087800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:141087200-141087800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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