Variant report

Variant	rs7647426
Chromosome Location	chr3:105084990-105084991
allele	C/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	chr3:105084988-105085903	A549	lung:	n/a	chr3:105085314-105085322 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
2	FOS	chr3:105084803-105085638	MCF10A-Er-Src	breast:	n/a	chr3:105085314-105085322 chr3:105085312-105085323 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
3	CBX3	chr3:105084925-105086039	HCT-116	colon:	n/a	n/a
4	CTCF	chr3:105084860-105085010	GM12871	blood:	n/a	n/a
5	SIN3AK20	chr3:105084834-105086152	MCF-7	breast:	n/a	n/a
6	NR3C1	chr3:105084962-105085849	A549	lung:	n/a	n/a
7	PBX3	chr3:105084919-105085944	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:105084812-105086180	HCT-116	colon:	n/a	n/a
9	SIN3AK20	chr3:105084561-105086326	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:105084872-105086371	Gliobla	brain:	n/a	n/a
11	GATA3	chr3:105084629-105086038	A549	lung:	n/a	chr3:105085402-105085412 chr3:105085186-105085196 chr3:105085312-105085321
12	CHD2	chr3:105084939-105086257	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:105084905-105086791	H1-hESC	embryonic stem cell:	n/a	n/a
14	BACH1	chr3:105084763-105086335	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:105084967-105085923	A549	lung:	n/a	n/a
16	FOSL2	chr3:105084501-105085876	A549	lung:	n/a	chr3:105085314-105085322 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
17	STAT3	chr3:105084630-105085253	MCF10A-Er-Src	breast:	n/a	chr3:105085241-105085253 chr3:105084756-105084776
18	RAD21	chr3:105084450-105086202	A549	lung:	n/a	chr3:105085505-105085515
19	MYC	chr3:105084236-105085998	A549	lung:	n/a	chr3:105085313-105085322 chr3:105085558-105085565
20	CTCF	chr3:105084840-105084990	GM12872	blood:	n/a	n/a
21	GATA3	chr3:105084642-105085931	SK-N-SH	brain:	n/a	chr3:105085402-105085412 chr3:105085186-105085196 chr3:105085312-105085321
22	FOXA2	chr3:105084832-105085510	A549	lung:	n/a	n/a
23	RAD21	chr3:105084234-105085870	SK-N-SH_RA	brain:	n/a	chr3:105085505-105085515
24	STAT3	chr3:105084683-105085691	MCF10A-Er-Src	breast:	n/a	chr3:105085241-105085253 chr3:105084756-105084776
25	CTCF	chr3:105084515-105084994	IMR90	lung:	n/a	n/a
26	POLR2A	chr3:105084469-105089450	MCF10A-Er-Src	breast:	n/a	n/a
27	EP300	chr3:105084774-105085891	A549	lung:	n/a	chr3:105085170-105085179 chr3:105085499-105085515
28	SMARCC1	chr3:105084954-105087287	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr3:105084537-105085593	A549	lung:	n/a	n/a
30	MAX	chr3:105084399-105089068	A549	lung:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
31	TAF1	chr3:105084920-105086133	ECC-1	luminal epithelium:	n/a	n/a
32	MAX	chr3:105084981-105085946	H1-hESC	embryonic stem cell:	n/a	chr3:105085313-105085322 chr3:105085558-105085565
33	HA-E2F1	chr3:105084461-105086434	MCF-7	breast:	n/a	n/a
34	POLR2A	chr3:105084982-105088897	Hela-S3	cervix:	n/a	n/a
35	MTA3	chr3:105084867-105088990	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:105084936-105088887	GM19193	blood:	n/a	n/a
37	MAX	chr3:105084930-105087138	ECC-1	luminal epithelium:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
38	MYBL2	chr3:105084963-105085907	HepG2	liver:	n/a	n/a
39	RAD21	chr3:105084946-105085953	A549	lung:	n/a	chr3:105085505-105085515
40	POLR2A	chr3:105084279-105085978	U87	brain:	n/a	n/a
41	BCL3	chr3:105084912-105085896	A549	lung:	n/a	chr3:105085314-105085323 chr3:105085313-105085322 chr3:105085509-105085518
42	TAF1	chr3:105084525-105085929	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr3:105084878-105089362	GM12891	blood:	n/a	n/a
44	POLR2A	chr3:105084135-105086196	HUVEC	blood vessel:	n/a	n/a
45	FOS	chr3:105083989-105085773	HUVEC	blood vessel:	n/a	chr3:105085314-105085322 chr3:105085312-105085323 chr3:105085486-105085495 chr3:105085313-105085323 chr3:105085312-105085324 chr3:105085313-105085323
46	MAX	chr3:105084946-105086144	A549	lung:	n/a	chr3:105085313-105085322 chr3:105085558-105085565
47	CTCF	chr3:105084960-105085110	HEEpiC	esophagus:	n/a	n/a
48	REST	chr3:105084317-105086022	A549	lung:	n/a	chr3:105085452-105085465 chr3:105084606-105084619 chr3:105085496-105085509
49	MAZ	chr3:105083603-105088618	IMR90	lung:	n/a	chr3:105085313-105085322 chr3:105086357-105086366 chr3:105085558-105085565
50	RAD21	chr3:105084867-105085891	H1-hESC	embryonic stem cell:	n/a	chr3:105085505-105085515

Variant related genes	Relation type
ALCAM	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11710166	0.87[ASN][1000 genomes]
rs11710857	0.84[ASN][1000 genomes]
rs11714275	0.87[ASN][1000 genomes]
rs11714277	0.90[ASN][1000 genomes]
rs11716035	0.90[ASN][1000 genomes]
rs11718405	0.90[ASN][1000 genomes]
rs11718457	0.90[ASN][1000 genomes]
rs11719817	0.90[ASN][1000 genomes]
rs1898655	0.87[ASN][1000 genomes]
rs1955135	0.87[ASN][1000 genomes]
rs2895300	0.90[ASN][1000 genomes]
rs34029528	0.90[ASN][1000 genomes]
rs59322590	0.87[ASN][1000 genomes]
rs61522255	0.87[ASN][1000 genomes]
rs6771935	0.90[ASN][1000 genomes]
rs6771987	0.90[ASN][1000 genomes]
rs6786815	0.90[ASN][1000 genomes]
rs6794273	0.87[ASN][1000 genomes]
rs73177459	0.82[ASN][1000 genomes]
rs73177465	0.90[ASN][1000 genomes]
rs73177470	0.90[ASN][1000 genomes]
rs73177478	0.90[ASN][1000 genomes]
rs73177489	0.90[ASN][1000 genomes]
rs73177494	0.90[ASN][1000 genomes]
rs73179378	0.90[ASN][1000 genomes]
rs73179384	0.90[ASN][1000 genomes]
rs73181374	0.90[ASN][1000 genomes]
rs73181376	0.90[ASN][1000 genomes]
rs73181380	0.90[ASN][1000 genomes]
rs73181387	0.90[ASN][1000 genomes]
rs73181395	0.90[ASN][1000 genomes]
rs73181396	0.90[ASN][1000 genomes]
rs73181397	0.90[ASN][1000 genomes]
rs73181401	0.90[ASN][1000 genomes]
rs73183103	0.90[ASN][1000 genomes]
rs73183108	0.87[ASN][1000 genomes]
rs73183112	0.87[ASN][1000 genomes]
rs73183114	0.87[ASN][1000 genomes]
rs73183115	0.87[ASN][1000 genomes]
rs73183185	0.87[ASN][1000 genomes]
rs73183186	0.87[ASN][1000 genomes]
rs73183187	0.87[ASN][1000 genomes]
rs73183188	0.87[ASN][1000 genomes]
rs73183198	0.87[ASN][1000 genomes]
rs73185114	0.87[ASN][1000 genomes]
rs73185115	0.87[ASN][1000 genomes]
rs7647531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105083600-105086400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:105083800-105087800	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:105083800-105088800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:105083800-105088800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:105084000-105085200	Flanking Active TSS	HUVEC	blood vessel
6	chr3:105084000-105085400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:105084000-105086200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:105084000-105087600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:105084000-105088800	Active TSS	Brain Substantia Nigra	brain
10	chr3:105084000-105089000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:105084000-105089000	Active TSS	A549	lung
12	chr3:105084000-105089600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:105084200-105085000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr3:105084200-105085000	Active TSS	Fetal Brain Male	brain
15	chr3:105084200-105085000	Active TSS	Fetal Brain Female	brain
16	chr3:105084200-105085400	Flanking Active TSS	HepG2	liver
17	chr3:105084200-105085800	Active TSS	Stomach Smooth Muscle	stomach
18	chr3:105084200-105087800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:105084200-105088400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:105084200-105089000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:105084200-105089000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:105084200-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:105084200-105089200	Active TSS	NHDF-Ad	bronchial
24	chr3:105084200-105089600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:105084200-105089600	Active TSS	NHLF	lung
26	chr3:105084200-105090400	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:105084400-105085000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:105084400-105085000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
29	chr3:105084400-105085000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
30	chr3:105084400-105085000	Active TSS	Fetal Stomach	stomach
31	chr3:105084400-105085200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
32	chr3:105084400-105085400	Flanking Active TSS	Liver	Liver
33	chr3:105084400-105085400	Flanking Active TSS	Colonic Mucosa	Colon
34	chr3:105084400-105085800	Bivalent/Poised TSS	Psoas Muscle	Psoas
35	chr3:105084400-105086000	Active TSS	Pancreas	Pancrea
36	chr3:105084400-105086000	Active TSS	Right Atrium	heart
37	chr3:105084400-105086200	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:105084400-105086200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:105084400-105086200	Active TSS	Colon Smooth Muscle	Colon
40	chr3:105084400-105086400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:105084400-105086400	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr3:105084400-105086600	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:105084400-105087200	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr3:105084400-105087800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:105084400-105088800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:105084400-105088800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:105084400-105088800	Active TSS	Brain Cingulate Gyrus	brain
48	chr3:105084400-105088800	Active TSS	Gastric	stomach
49	chr3:105084400-105089000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:105084400-105089000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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